5. Beta diversity
INFO
This Rmarkdown contains the commands necessary to perform beta diversity analysis of the output from the DF_GMH_PIPELINE. It is expected that the data has been imported, cleaned, and saved following the script 1_Import.Rmd prior to using this script.
Beta diversity, also called “between sample diversity” is calculated as a dissimilarity distance between individual samples. Here we calculate metrices: - Bray-Curtis - Jaccard - UniFrac - Unweighted UniFrac - Aitchison (not used in final presentation)
SETUP
CALCULATE DISTANCES
PREPARE DATA
First step is to create a clean phyloseq object (remove samples missing relevant data and/or subset by a relevant variable).
Beta diversity are affected by all samples included, so if some samples are removed, this should preferably be done before the beta diversity is calculated. > qualitative metrics are sensitive to sequencing depth, so rarefaction should be done for those metrics as well.
CALCULATE
There are many different algorithms that can be used to calculate beta diversity. Each metric has its own advantages and many times a comparison of the results from two metrics tells more about the data than each one separately. I will include phylogeny based (UniFrac and weighted UniFrac), qualitative (presence/absence), quantitative (abundance based), and compositional (Aitchison) metrics in this template
UNWEIGHTED UNIFRAC
The unique fraction metric, or UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both (Lozupone & Knight, 2005). This metric is sensitive to sequencing depth, so it is required to use a rarefied phyloseq object The UniFrac algorithm requires a rooted tree, so if ASVs has been removed from the raw da the tree should be rerooted manually, else a random ASV will be chosen as root.
MTRLS <- c("Feces","Cecum","Ileum","Cecum_HF","Ileum_HF","Cecum_LF","Ileum_LF","Feces_no20","Feces_no020","Feces_HF","Feces_LF","Feces_HF_no0","Feces_LF_no0","Feces_HF_d08","Feces_LF_d08","Feces_HF-CTRL_d08","Feces_LF-CTRL_d08","Feces_HF-PFOS_d08","Feces_LF-PFOS_d08")
# load
params <- readRDS("R_objects/params_betadiv.RDS")
for (MTRL in MTRLS) {
load(paste0("R_objects/Phyloseq_betadiv_",MTRL,".Rdata"))
message(paste0("Calcualting distances for ",MTRL,"..."))
# Calculate UniFrac distances
unif.dist <- UniFrac(phy.rare, weighted = FALSE, parallel = FALSE)
# Calculate PCoA data
unif.pcoa <- ordinate(phy.rare, method = "PCoA",distance = unif.dist)
unif.nmds <- metaMDS(unif.dist, k = 5, trymax = 1000)
# Save distance objects
save(unif.dist, unif.nmds, unif.pcoa, phy.rare, file = paste0("R_objects/bdiv_unif_",MTRL,".RData"))
}
# clear the environment and release memory
rm(list = ls(all.names = TRUE))
invisible(gc())WEIGHTED UNIFRAC
The unique fraction metric, or UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both (Lozupone & Knight, 2005). Weighted UniFrac takes the abundance of each ASV into account instead of just presence/absence, which means that it will not be sensitive to sequencing depth. The UniFrac algorithm requires a rooted tree, so if ASVs has been removed from the raw da the tree should be rerooted manually, else a random ASV will be chosen as root.
MTRLS <- c("Feces","Cecum","Ileum","Cecum_HF","Ileum_HF","Cecum_LF","Ileum_LF","Feces_no20","Feces_no020","Feces_HF","Feces_LF","Feces_HF_no0","Feces_LF_no0","Feces_HF_d08","Feces_LF_d08","Feces_HF-CTRL_d08","Feces_LF-CTRL_d08","Feces_HF-PFOS_d08","Feces_LF-PFOS_d08")
# load
params <- readRDS("R_objects/params_betadiv.RDS")
for (MTRL in MTRLS) {
load(paste0("R_objects/Phyloseq_betadiv_",MTRL,".Rdata"))
message(paste0("Calcualting distances for ",MTRL,"..."))
# Calculate UniFrac distances
wuf.dist <- UniFrac(phy.clean, weighted = TRUE, parallel = FALSE)
# Calculate PCoA data
wuf.pcoa <- ordinate(phy.clean, method = "PCoA",distance = wuf.dist)
wuf.nmds <- metaMDS(wuf.dist, k = 5, trymax = 1000)
# Save distance objects
save(wuf.dist, wuf.nmds, wuf.pcoa, phy.clean, file = paste0("R_objects/bdiv_wuf_",MTRL,".RData"))
}
# clear the environment and release memory
rm(list = ls(all.names = TRUE))
invisible(gc())BRAY-CURTIS
Bray-Curtis dissimilarity index (as implemented by the vegan package) is the sum of abundance difference for each species/ASV, divided by theoretical maximum difference between the samples if no ASV overlapped. The formula used is: \[d_{jk} = \frac{\sum|n_{ij}-n_{ik}|}{\sum(n_{ij}+n_{ik})}\] Bray-Curtis dissimilarity is not a true distance metric as it does not adhere to the triangle inequality, but is often used to compare microbiomes. Bray-Curtis dissimilarities are based on the assumption that measurements are taken from equal areas, so differences in total counts between samples will bias the metric. As differences in sequences depth is due to differences in the lab procedures and not biological differences, we should transform our counts to relative abundances before calculating Bray-Curtis dissimilarities. By transforming the data to abundances no data is lost, but rarefied data can also be used.
MTRLS <- c("Feces","Cecum","Ileum","Cecum_HF","Ileum_HF","Cecum_LF","Ileum_LF","Feces_no20","Feces_no020","Feces_HF","Feces_LF","Feces_HF_no0","Feces_LF_no0","Feces_HF_d08","Feces_LF_d08","Feces_HF-CTRL_d08","Feces_LF-CTRL_d08","Feces_HF-PFOS_d08","Feces_LF-PFOS_d08")
# load
params <- readRDS("R_objects/params_betadiv.RDS")
for (MTRL in MTRLS) {
load(paste0("R_objects/Phyloseq_betadiv_",MTRL,".Rdata"))
message(paste0("Calcualting distances for ",MTRL,"..."))
# transform counts
phy.ra <- transform_sample_counts(phy.clean, function(x) x/sum(x))
# Calculate Bray-Curtis dissimilarities
bray.dist <- distance(phy.ra, method = "bray",)
# Calculate PCoA data
bray.pcoa <- ordinate(phy.ra, method = "PCoA",distance = bray.dist)
bray.nmds <- metaMDS(bray.dist, k = 5, trymax = 1000)
# Save distance objects
save(bray.dist, bray.nmds, bray.pcoa, phy.ra, file = paste0("R_objects/bdiv_bray_",MTRL,".RData"))
}
# clear the environment and release memory
rm(list = ls(all.names = TRUE))
invisible(gc())JACCARD
The Jaccard similarity measures the similarity between two sets of data to see which members are shared and distinct. The Jaccard similarity is calculated by dividing the number of observations in both sets by the number of observations in either set. In other words, the Jaccard similarity can be computed as the size of the intersection divided by the size of the union of two sets. This can be written in set notation using intersection \((A \cap B)\) and unions \((A \cup B)\) of two sets: \[J(A,B) = \frac{|A \cap B|}{|A \cup B|}\] where \(|A \cap B|\) gives the number of members shared between both sets and \(|A \cup B|\) gives the total number of members in both sets (shared and un-shared). The Jaccard Similarity will be 0 if the two sets don’t share any values and 1 if the two sets are identical.
Additionally, this function can be used to find the dissimilarity between two sets by calculating: \[d(A,B) = 1 - J(A,B)\] > We will be calculating binary Jaccard dissimilarity
MTRLS <- c("Feces","Cecum","Ileum","Cecum_HF","Ileum_HF","Cecum_LF","Ileum_LF","Feces_no20","Feces_no020","Feces_HF","Feces_LF","Feces_HF_no0","Feces_LF_no0","Feces_HF_d08","Feces_LF_d08","Feces_HF-CTRL_d08","Feces_LF-CTRL_d08","Feces_HF-PFOS_d08","Feces_LF-PFOS_d08")
# load
params <- readRDS("R_objects/params_betadiv.RDS")
for (MTRL in MTRLS) {
load(paste0("R_objects/Phyloseq_betadiv_",MTRL,".Rdata"))
message(paste0("Calcualting distances for ",MTRL,"..."))
# Calculate Jaccard binary dissimilarities
jac.dist <- distance(phy.rare, method = "jaccard", binary = TRUE)
# Calculate PCoA data
jac.pcoa <- ordinate(phy.rare, method = "PCoA",distance = jac.dist)
jac.nmds <- metaMDS(jac.dist, k = 5, trymax = 1000)
# Save distance objects
save(jac.dist, jac.nmds, jac.pcoa, phy.rare, file = paste0("R_objects/bdiv_jac_",MTRL,".RData"))
}
# clear the environment and release memory
rm(list = ls(all.names = TRUE))
invisible(gc())AITCHISON
Aitchison distance (1986) and robust Aitchison distance (Martino et al. 2019) are metrics that deal with compositional data. The Aitchison distance is a dissimilarity measure calculated as the Euclidean distance between observations (samples) after performing a centered log ratio (“clr”) transformation. Aitchison distance has been said to outperform Jensen-Shannon divergence and Bray-Curtis dissimilarity, due to a better stability to subsetting and aggregation, and it being a proper distance (Aitchison et al., 2000).
MTRLS <- c("Feces","Cecum","Ileum","Cecum_HF","Ileum_HF","Cecum_LF","Ileum_LF","Feces_no20","Feces_no020","Feces_HF","Feces_LF","Feces_HF_no0","Feces_LF_no0","Feces_HF_d08","Feces_LF_d08","Feces_HF-CTRL_d08","Feces_LF-CTRL_d08","Feces_HF-PFOS_d08","Feces_LF-PFOS_d08")
# load
params <- readRDS("R_objects/params_betadiv.RDS")
for (MTRL in MTRLS) {
load(paste0("R_objects/Phyloseq_betadiv_",MTRL,".Rdata"))
message(paste0("Calcualting distances for ",MTRL,"..."))
# Calculate Bray-Curtis dissimilarities
ait.dist <- vegan::vegdist(otu_table(phy.clean), method = "robust.aitchison")
# Calculate PCoA data
ait.pcoa <- ordinate(phy.clean, method = "PCoA",distance = ait.dist)
ait.nmds <- metaMDS(ait.dist, k = 5, trymax = 1000)
# Save distance objects
save(ait.dist, ait.nmds, ait.pcoa, phy.clean, file = paste0("R_objects/bdiv_ait_",MTRL,".RData"))
}
# clear the environment and release memory
rm(list = ls(all.names = TRUE))
invisible(gc())SUBSETS PER DAY AND FEED
Running subsets for downstream analysis.
METRICES <- c("bray","unif","wuf","jac","ait")
DAYS <- c("d0","d08","d12","d16","d20","d21")
FEEDS <- c("HF","LF","ALL")
MTRLS <- c("Feces","Cecum","Ileum")
# load
params <- readRDS("R_objects/params_betadiv.RDS")
#load("R_objects/Phyloseq_betadiv.Rdata")
for (MTRL in MTRLS) {
message(paste0("Running loop for calculation of beta diversity subsets for ",MTRL,"."))
if (MTRL == "Cecum" || MTRL == "Ileum") {
DAYS <- c("d08","d21")
} else if (MTRL == "Feces") {
DAYS <- c(,"d0","d08","d12","d16","d20","d21")
}
for (DAY in DAYS) {
print(paste0("Processing day ",DAY,"..."))
for (FEED in FEEDS) {
for (METRIC in METRICES) {
load(paste0("R_objects/Phyloseq_betadiv_",MTRL,".Rdata"))
if (FEED == "ALL") {
FILENAME <- paste0("R_objects/bdiv_sub_",MTRL,"_",DAY,"_",METRIC,".Rdata")
} else {
FILENAME <- paste0("R_objects/bdiv_sub_",MTRL,"_",DAY,"_",FEED,"_",METRIC,".Rdata")
}
if (METRIC == "unif") {
load(paste0("R_objects/bdiv_unif_",MTRL,".RData"))
tmp.dist <- as.matrix(unif.dist)
if (FEED == "ALL") {
phy.sub <- subset_samples(phy.rare, material == MTRL & day %in% DAY)
} else {
phy.sub <- subset_samples(phy.rare, material == MTRL & day %in% DAY & feed %in% FEED)
}
SUBS <- sample_names(phy.sub)
tmp.sub.dist <- tmp.dist[SUBS, SUBS]
unif.sub.dist <- as.dist(tmp.sub.dist, diag = TRUE, upper = TRUE)
unif.sub.pcoa <- ordinate(phy.sub, method = "PCoA",distance = unif.sub.dist)
unif.sub.nmds <- metaMDS(unif.sub.dist, k = 5, trymax = 1000)
save(phy.sub, unif.sub.dist, unif.sub.nmds, unif.sub.pcoa, file = FILENAME)
} else if (METRIC == "wuf") {
load(paste0("R_objects/bdiv_wuf_",MTRL,".RData"))
tmp.dist <- as.matrix(wuf.dist)
if (FEED == "ALL") {
phy.sub <- subset_samples(phy.clean, material == MTRL & day %in% DAY)
} else {
phy.sub <- subset_samples(phy.clean, material == MTRL & day %in% DAY & feed %in% FEED)
}
SUBS <- sample_names(phy.sub)
tmp.sub.dist <- tmp.dist[SUBS, SUBS]
wuf.sub.dist <- as.dist(tmp.sub.dist, diag = TRUE, upper = TRUE)
wuf.sub.pcoa <- ordinate(phy.sub, method = "PCoA",distance = wuf.sub.dist)
wuf.sub.nmds <- metaMDS(wuf.sub.dist, k = 5, trymax = 1000)
save(phy.sub, wuf.sub.dist, wuf.sub.nmds, wuf.sub.pcoa, file = FILENAME)
} else if (METRIC == "bray") {
load(paste0("R_objects/bdiv_bray_",MTRL,".RData"))
tmp.dist <- as.matrix(bray.dist)
if (FEED == "ALL") {
phy.sub <- subset_samples(phy.rare, material == MTRL & day %in% DAY)
} else {
phy.sub <- subset_samples(phy.rare, material == MTRL & day %in% DAY & feed %in% FEED)
}
SUBS <- sample_names(phy.sub)
tmp.sub.dist <- tmp.dist[SUBS, SUBS]
bray.sub.dist <- as.dist(tmp.sub.dist, diag = TRUE, upper = TRUE)
bray.sub.pcoa <- ordinate(phy.sub, method = "PCoA", distance = bray.sub.dist)
bray.sub.nmds <- metaMDS(bray.sub.dist, k = 5, trymax = 1000)
save(phy.sub, bray.sub.dist, bray.sub.pcoa, bray.sub.nmds, file = FILENAME)
} else if (METRIC == "jac") {
load(paste0("R_objects/bdiv_jac_",MTRL,".RData"))
tmp.dist <- as.matrix(jac.dist)
if (FEED == "ALL") {
phy.sub <- subset_samples(phy.rare, material == MTRL & day %in% DAY)
} else {
phy.sub <- subset_samples(phy.rare, material == MTRL & day %in% DAY & feed %in% FEED)
}
SUBS <- sample_names(phy.sub)
tmp.sub.dist <- tmp.dist[SUBS, SUBS]
jac.sub.dist <- as.dist(tmp.sub.dist, diag = TRUE, upper = TRUE)
jac.sub.pcoa <- ordinate(phy.sub, method = "PCoA", distance = jac.sub.dist)
jac.sub.nmds <- metaMDS(jac.sub.dist, k = 5, trymax = 1000)
save(phy.sub, jac.sub.dist, jac.sub.pcoa, jac.sub.nmds, file = FILENAME)
} else if (METRIC == "ait") {
load(paste0("R_objects/bdiv_ait_",MTRL,".RData"))
tmp.dist <- as.matrix(ait.dist)
if (FEED == "ALL") {
phy.sub <- subset_samples(phy.clean, material == MTRL & day %in% DAY)
} else {
phy.sub <- subset_samples(phy.clean, material == MTRL & day %in% DAY & feed %in% FEED)
}
SUBS <- sample_names(phy.sub)
tmp.sub.dist <- tmp.dist[SUBS, SUBS]
ait.sub.dist <- as.dist(tmp.sub.dist, diag = TRUE, upper = TRUE)
ait.sub.pcoa <- ordinate(phy.sub, method = "PCoA", distance = ait.sub.dist)
ait.sub.nmds <- metaMDS(ait.sub.dist, k = 5, trymax = 1000)
save(phy.sub, ait.sub.dist, ait.sub.pcoa, ait.sub.nmds, file = FILENAME)
}
}
}
}
}
# clear the environment and release memory
rm(list = ls(all.names = TRUE))
invisible(gc())VISUALIZATION (TIMELINE)
Beta diversity is generally visualized by a NMDS (non metric multidimensional scaling) or PCoA (Principal Coordinate Analysis) plots. Both methods creates a representation of the beta diversity on few axes (3D plots should only be used for interactive on screen representations). Here we have chosen to present in PCoA. Distance separation is based on Axis 1 and 2 as these provide the clearest distances of the analyses.
ANALYSES FOR ALL SUBSETS
The following block runs processing and presentation for all distance metrices subsets of interest along with statistical support through PERMANOVA. These subsets include the following (Note: day 20 is excluded for all sets):
- Feces samples
- All samples
- Without Day 0
- Separated by diet (HF and LF)
- Without Day 0
- Separated by treatment (CTRL and PFOS)
- Isolated Day 0 and 8
- All days excluding Day 0 (due to significant difference in LF DAy 0 data)
- All samples
- Ileum samples
- All samples
- Separated by diet (HF and LF)
- Cecum samples
- All samples
- Separated by diet (HF and LF)
Analyses includes ordination analysis (PCoA), PERMANOVA and test for effect from dispersion (betadisper), as well as plotting.
params <- readRDS("R_objects/params_betadiv.RDS")
# Define Metrices
METRICES <- c("bray","jac","unif","wuf")
# Define Subsets to analyse
MTRLS <- c("Feces_no20","Feces_no020","Feces_HF","Feces_HF_no0","Feces_HF_d08","Feces_LF","Feces_LF_no0","Feces_LF_d08","Feces_HF-CTRL_d08","Feces_LF-CTRL_d08","Feces_HF-PFOS_d08","Feces_LF-PFOS_d08","Cecum","Cecum_HF","Cecum_LF","Ileum","Ileum_HF","Ileum_LF")
# Run loop
for (MTRL in MTRLS) {
for (METRIC in METRICES) {
print(paste0("Processing ",MTRL," ",METRIC," data..."))
# Choose variable
VAR <- "feed_treat_day"
# Load data based on metric
if (METRIC == "unif") {
load(paste0("R_objects/bdiv_unif_",MTRL,".RData"))
dist.used <- unif.dist
nmds.used <- unif.nmds
pcoa.used <- unif.pcoa
phy.used <- phy.rare
rm(unif.dist, unif.nmds, unif.pcoa, phy.rare)
} else if (METRIC == "wuf") {
load(paste0("R_objects/bdiv_wuf_",MTRL,".RData"))
dist.used <- wuf.dist
nmds.used <- wuf.nmds
pcoa.used <- wuf.pcoa
phy.used <- phy.clean
rm(wuf.dist, wuf.nmds, wuf.pcoa,phy.clean)
} else if (METRIC == "bray"){
load(paste0("R_objects/bdiv_bray_",MTRL,".RData"))
dist.used <- bray.dist
nmds.used <- bray.nmds
pcoa.used <- bray.pcoa
phy.used <- phy.ra
rm(bray.dist, bray.nmds, bray.pcoa, phy.ra)
} else if (METRIC == "jac"){
load(paste0("R_objects/bdiv_jac_",MTRL,".RData"))
dist.used <- jac.dist
nmds.used <- jac.nmds
pcoa.used <- jac.pcoa
phy.used <- phy.rare
rm(jac.dist, jac.nmds, jac.pcoa, phy.rare)
} else if (METRIC == "ait"){
load(paste0("R_objects/bdiv_ait_",MTRL,".RData"))
dist.used <- ait.dist
nmds.used <- ait.nmds
pcoa.used <- ait.pcoa
phy.used <- phy.clean
rm(ait.dist, ait.nmds, ait.pcoa, phy.clean)
}
# Extract metadata from phyloseq
mdat <- data.frame(sample_data(phy.used))
# If a variable consist of numbers, but represent distinct groups remember to make it into a factor
mdat[,VAR] <- as.factor(mdat[,VAR])
COL_DFT <- c("0_HF_CTRL" = "#e4fadd","8_HF_CTRL" = "#d2e9cc", "12_HF_CTRL" = "#9fd3a3", "16_HF_CTRL" = "#65bf76", "21_HF_CTRL" = "#32a248",
"0_HF_PFOS" = "#d2e9cc","8_HF_PFOS" = "#9fd3a3", "12_HF_PFOS" = "#65bf76", "16_HF_PFOS" = "#32a248", "21_HF_PFOS" = "#108026",
"0_LF_CTRL" = "#def8fd", "8_LF_CTRL" = "#bde7fb", "12_LF_CTRL" = "#86c1e5", "16_LF_CTRL" = "#509cce", "21_LF_CTRL" = "#1879b7",
"0_LF_PFOS" = "#bde7fb", "8_LF_PFOS" = "#86c1e5", "12_LF_PFOS" = "#509cce", "16_LF_PFOS" = "#1879b7", "21_LF_PFOS" = "#065795")
COL_DF <- c("HF_d0" = "#d2e9cc","HF_d08" = "#9fd3a3", "HF_d12" = "#65bf76", "HF_d16" = "#32a248", "HF_d21" = "#108026",
"LF_d0" = "#bde7fb", "LF_d08" = "#86c1e5", "LF_d12" = "#509cce", "LF_d16" = "#1879b7", "LF_d21" = "#065795")
# Create plots of eigenvalues for PCoA plots
pcoa.tab <- plot_ordination(phy.used, pcoa.used,axes = 1:5,justDF = TRUE)
nmds.tab <- plot_ordination(phy.used, nmds.used,axes = 1:5,justDF = TRUE)
# Reformat tables to create one common table
colnames(nmds.tab)[1:5] <- c("Axis.1","Axis.2","Axis.3","Axis.4","Axis.5")
nmds.tab$ordination <- "nmds"
pcoa.tab$ordination <- "pcoa"
# Calculate centroids in PCOA
centroid.1 <- pcoa.tab %>% group_by(across(all_of("feed_treat_day"))) %>% get_summary_stats("Axis.1", type = "mean")
centroid.1 <- subset(centroid.1, select = -c(variable,n))
colnames(centroid.1)[1:2] <- c("feed_treat_day","X")
centroid.2 <- pcoa.tab %>% group_by(across(all_of("feed_treat_day"))) %>% get_summary_stats("Axis.2", type = "mean")
centroid.2 <- subset(centroid.2, select = -c(feed_treat_day,variable,n))
colnames(centroid.2)[1] <- "Y"
centroid <- cbind(centroid.1,centroid.2)
centroid <- centroid %>% mutate("day" = case_when(grepl("0_",feed_treat_day) ~ "d0",
grepl("8_",feed_treat_day) ~ "d08",
grepl("12_",feed_treat_day) ~ "d12",
grepl("16_",feed_treat_day) ~ "d16",
grepl("21_",feed_treat_day) ~ "d21"),
"label" = case_when(grepl("0_",feed_treat_day) ~ "Day 0",
grepl("8_",feed_treat_day) ~ "Day 8",
grepl("12_",feed_treat_day) ~ "Day 12",
grepl("16_",feed_treat_day) ~ "Day 16",
grepl("21_",feed_treat_day) ~ "Day 21",))
centroid <- centroid %>% mutate("feed_treat" = case_when(grepl("HF_CTRL",feed_treat_day) ~ "HF_CTRL",
grepl("HF_PFOS",feed_treat_day) ~ "HF_PFOS",
grepl("LF_CTRL",feed_treat_day) ~ "LF_CTRL",
grepl("LF_PFOS",feed_treat_day) ~ "LF_PFOS"))
centroid <- centroid %>% mutate("treat" = case_when(grepl("_CTRL",feed_treat_day) ~ "CTRL",
grepl("_PFOS",feed_treat_day) ~ "PFOS"))
centroid <- centroid %>% mutate("feed" = case_when(grepl("HF_",feed_treat_day) ~ "HF",
grepl("LF_",feed_treat_day) ~ "LF"))
centroid <- centroid %>% mutate("coord" = case_when(day == "d0" ~ "x1",
day == "d08" ~ "x2",
day == "d12" ~ "x3",
day == "d16" ~ "x4",
day == "d21" ~ "x5"))
centroid <- centroid[order(centroid$day),]
ord.tab <- rbind(nmds.tab,pcoa.tab)
ord.tab[,VAR] <- as.factor(ord.tab[,VAR])
# Melt axis to be in one variable
axis.tab <- pivot_longer(data = ord.tab, cols = c("Axis.1","Axis.2","Axis.3","Axis.4","Axis.5"), names_to = "Axis", values_to = "position")
# Plot PCoA - Split by Grouping
pcoa.plot <- ggplot(data = ord.tab[ord.tab$ordination == "pcoa",], aes_string(x = "Axis.1", y = "Axis.2", color = "feed_day")) +
stat_ellipse(aes_string(x = "Axis.1", y = "Axis.2", color = "feed_day", fill = "feed_day"), geom = "polygon", alpha = 0.1, level = 0.9) +
geom_point() +
geom_path(data = centroid, aes_string(x = "X", y = "Y", color = "feed_day"), color = "#222222", size = 0.5, alpha = 0.8, arrow = arrow(type = "closed", length = unit(2.5,"mm"))) +
geom_point(data = centroid, aes_string(x = "X", y = "Y", color = "feed_day"), color = "#555555", shape = 20, size = 3, alpha = 1) +
geom_text_repel(data = centroid, mapping = aes(x = X, y = Y), label = centroid$label, size = 4, min.segment.length = 0, segment.alpha = 0.8, box.padding = 1, force = 1, color = "#222222", position = "identity", direction = "both") +
theme_pubr() +
scale_color_manual(values = COL_DF) +
scale_fill_manual(values = COL_DF, name = "Feed + Day",
labels = c("HF_d0" = "HF 0","HF_d08" = "HF 8", "HF_d12" = "HF 12", "HF_d16" = "HF 16", "HF_d21" = "HF 21",
"LF_d0" = "LF 0", "LF_d08" = "LF 8", "LF_d12" = "LF 12", "LF_d16" = "LF 16", "LF_d21" = "LF 21"),
breaks = c("HF_d0","LF_d0","HF_d08","LF_d08","HF_d12","LF_d12","HF_d16","LF_d16","HF_d21","LF_d21")) +
facet_wrap(.~feed_treat, labeller = labeller(feed_treat = c("LF_CTRL" = "LF-CTRL","LF_PFOS" = "LF-PFOS","HF_CTRL" = "HF-CTRL","HF_PFOS" = "HF-PFOS"))) +
scale_y_continuous() +
labs(x = "PCoA 1", y = "PCoA 2") +
guides(color = "none", fill = guide_legend(override.aes = list(alpha = 1, byrow = TRUE, direction = "horizontal")))
pcoa.plot
if (MTRL %in% c("Feces_no20","Feces_no020","Cecum","Ileum")) {
# Plot PCoA - Split by Treatment
pcoa.treat <- ggplot(data = ord.tab[ord.tab$ordination == "pcoa",], aes_string(x = "Axis.1", y = "Axis.2")) +
stat_ellipse(aes_string(x = "Axis.1", y = "Axis.2", color = "feed_treat", fill = "feed_day"), geom = "polygon", alpha = 0.1, level = 0.9) +
geom_point(aes_string(color = "feed_treat", shape = "day")) +
theme_pubr() +
scale_color_manual(values = params$COL, name = "Group",
labels = c("LF_CTRL" = "LF-CTRL","LF_PFOS" = "LF-PFOS","HF_CTRL" = "HF-CTRL","HF_PFOS" = "HF-PFOS")) +
scale_fill_manual(values = COL_DF, name = "Feed + Day",
labels = c("HF_d0" = "HF 0","HF_d08" = "HF 8", "HF_d12" = "HF 12", "HF_d16" = "HF 16", "HF_d21" = "HF 21",
"LF_d0" = "LF 0", "LF_d08" = "LF 8", "LF_d12" = "LF 12", "LF_d16" = "LF 16", "LF_d21" = "LF 21"),
breaks = c("HF_d0","LF_d0","HF_d08","LF_d08","HF_d12","LF_d12","HF_d16","LF_d16","HF_d21","LF_d21")) +
scale_shape_manual(values = c("d0" = 3, "d08" = 19, "d12" = 1, "d16" = 17, "d21" = 2), name = "Day", labels = c("d0" = "0", "d08" = "8", "d12" = "12", "d16" = "16", "d21" = "21")) +
facet_wrap(.~treatment) +
scale_y_continuous() +
labs(x = "PCoA 1", y = "PCoA 2") +
guides(fill = "none", shape = guide_legend(override.aes = list(size = 3), order = 2), color = guide_legend(override.aes = list(shape = NA, fill = params$COL, alpha = 1, linetype = c(0,0)), order = 1))#guide_legend(override.aes = list(alpha = 1, byrow = TRUE, direction = "horizontal")))
pcoa.treat
# Plot PCoA - Split by Diet
pcoa.diet <- ggplot(data = ord.tab[ord.tab$ordination == "pcoa",], aes_string(x = "Axis.1", y = "Axis.2")) +
stat_ellipse(aes_string(x = "Axis.1", y = "Axis.2", color = "feed_treat", fill = "feed_treat"), geom = "polygon", alpha = 0.1, level = 0.9) +
geom_point(aes_string(color = "feed_treat", shape = "day")) +
theme_pubr() +
scale_color_manual(values = params$COL, name = "Group",
labels = c("LF_CTRL" = "LF-CTRL","LF_PFOS" = "LF-PFOS","HF_CTRL" = "HF-CTRL","HF_PFOS" = "HF-PFOS")) +
scale_fill_manual(values = params$COL, name = "Group") +
scale_shape_manual(values = c("d0" = 3, "d08" = 19, "d12" = 1, "d16" = 17, "d21" = 2), name = "Day", labels = c("d0" = "0", "d08" = "8", "d12" = "12", "d16" = "16", "d21" = "21")) +
facet_wrap(.~feed, scales = "free") +
scale_y_continuous() +
labs(x = "PCoA 1", y = "PCoA 2") +
guides(fill = "none", shape = guide_legend(override.aes = list(size = 3), order = 2), color = guide_legend(override.aes = list(shape = NA, fill = params$COL, alpha = 1, linetype = c(0,0)), order = 1))#guide_legend(override.aes = list(alpha = 1, byrow = TRUE, direction = "horizontal")))
pcoa.diet
# Rename
if (METRIC == "bray") {
bray.treat <- pcoa.treat
bray.diet <- pcoa.diet
} else if (METRIC == "jac") {
jac.treat <- pcoa.treat
jac.diet <- pcoa.diet
} else if (METRIC == "unif") {
unif.treat <- pcoa.treat
unif.diet <- pcoa.diet
} else if (METRIC == "wuf") {
wuf.treat <- pcoa.treat
wuf.diet <- pcoa.diet
} else if (METRIC == "ait") {
ait.treat <- pcoa.treat
ait.diet <- pcoa.diet
}
# Save extra plots
suppressMessages(ggsave(filename = paste0("plots/bdiv/timeline/",MTRL,"/bdiv_treat_",MTRL,"_",METRIC,".png"), plot = pcoa.treat, device = "png", dpi = 300, units = "mm", height = 110, width = 200))
suppressMessages(ggsave(filename = paste0("plots/bdiv/timeline/",MTRL,"/bdiv_treat_",MTRL,"_",METRIC,".pdf"), plot = pcoa.treat, device = "pdf", dpi = 300, units = "mm", height = 110, width = 200))
suppressMessages(ggsave(filename = paste0("plots/bdiv/timeline/",MTRL,"/bdiv_diet_",MTRL,"_",METRIC,".png"), plot = pcoa.diet, device = "png", dpi = 300, units = "mm", height = 110, width = 200))
suppressMessages(ggsave(filename = paste0("plots/bdiv/timeline/",MTRL,"/bdiv_diet_",MTRL,"_",METRIC,".pdf"), plot = pcoa.diet, device = "pdf", dpi = 300, units = "mm", height = 110, width = 200))
} else {print("No extra plots...")}
# Calculate PERMANOVA
## Note: use of column variable "PFOS" rather than "treatment", as this variable reflects direct PFOS exposure on all days and not just treatment grouping - this is important to detect impact of PFOS longitudinally as HF-PFOS and LF-PFOS has not been exposed on day 0.
if (MTRL %in% c("Feces_HF","Feces_LF","Feces_HF_no0","Feces_LF_no0","Feces_HF_d08","Feces_LF_d08","Cecum_HF","Cecum_LF","Ileum_HF","Ileum_LF")) {
perm <- adonis2(dist.used ~ day*PFOS, data = mdat, permutations = 999, na.action = na.omit)
} else if (MTRL %in% c("Feces_HF-CTRL_d08","Feces_LF-CTRL_d08","Feces_HF-PFOS_d08","Feces_LF-PFOS_d08")) {
perm <- adonis2(dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
} else if (MTRL == "Feces_no020"){
perm <- adonis2(dist.used ~ feed*PFOS, data = mdat, permutations = 999, na.action = na.omit)
} else {
perm <- adonis2(dist.used ~ day*feed*PFOS, data = mdat, permutations = 999, na.action = na.omit)
}
# DISPERTION
## First we will test the beta diversity dispertion to determine whether any differences in dispertion might cause any PERMANOVA differences.
# Calculate beta-dispertion
bdisp <- betadisper(dist.used, mdat[,VAR])
plot(bdisp)
# Run statical test
aov <- anova(bdisp) # not significant
# Run posthoc test if significant and more than two groups
thsd <- TukeyHSD(bdisp)
plot(TukeyHSD(bdisp))
# Plot dispertion
boxplot(bdisp)
## When plotting the TukeyHSD, the y-axis is terribly formatted, but ordered similarly to the written output.
# Print output for loop
print(plot(bdisp))
print(aov)
print(pcoa.plot)
print(paste0("PERMANOVA RESULTS FOR: ",METRIC))
print(perm)
print("")
if (METRIC == "bray") {
bray.plot <- pcoa.plot
bray.perm <- perm
} else if (METRIC == "jac") {
jac.plot <- pcoa.plot
jac.perm <- perm
} else if (METRIC == "unif") {
unif.plot <- pcoa.plot
unif.perm <- perm
} else if (METRIC == "wuf") {
wuf.plot <- pcoa.plot
wuf.perm <- perm
} else if (METRIC == "ait") {
ait.plot <- pcoa.plot
ait.perm <- perm
}
# Save PERMANOVA as txt file
if (!file.exists(paste0("plots/bdiv/timeline/",MTRL))) dir.create(file.path(getwd(), paste0("plots/bdiv/timeline/",MTRL)))
write.table(perm, file = paste0("plots/bdiv/timeline/",MTRL,"/perm_timeline_",MTRL,"_",METRIC,".txt"))
write.table(aov, file = paste0("plots/bdiv/timeline/",MTRL,"/aov_timeline_",MTRL,"_",METRIC,".txt"))
# Save plot
if (MTRL %in% c("Feces_no20","Cecum","Ileum")) {
suppressMessages(ggsave(filename = paste0("plots/bdiv/timeline/",MTRL,"/bdiv_timeline_",MTRL,"_",METRIC,".png"), plot = pcoa.plot, device = "png", dpi = 300, units = "mm", height = 200, width = 200))
suppressMessages(ggsave(filename = paste0("plots/bdiv/timeline/",MTRL,"/bdiv_timeline_",MTRL,"_",METRIC,".pdf"), plot = pcoa.plot, device = "pdf", dpi = 300, units = "mm", height = 200, width = 200))
} else {
suppressMessages(ggsave(filename = paste0("plots/bdiv/timeline/",MTRL,"/bdiv_timeline_",MTRL,"_",METRIC,".png"), plot = pcoa.plot, device = "png", dpi = 300, units = "mm", height = 170, width = 150))
suppressMessages(ggsave(filename = paste0("plots/bdiv/timeline/",MTRL,"/bdiv_timeline_",MTRL,"_",METRIC,".pdf"), plot = pcoa.plot, device = "pdf", dpi = 300, units = "mm", height = 170, width = 150))
}
}
if (MTRL %in% c("Feces_no20","Feces_no020","Cecum","Ileum")) {
save(bray.perm,bray.plot,jac.perm,jac.plot,unif.perm,unif.plot,wuf.perm,wuf.plot,bray.treat,bray.diet,jac.treat,jac.diet,unif.treat,unif.diet,wuf.treat,wuf.diet, file = paste0("plots/bdiv/timeline/",MTRL,"/PCoA_plot_",MTRL,".Rdata"))
} else {
save(bray.perm,bray.plot,jac.perm,jac.plot,unif.perm,unif.plot,wuf.perm,wuf.plot, file = paste0("plots/bdiv/timeline/",MTRL,"/PCoA_plot_",MTRL,".Rdata"))
}
}## [1] "Processing Feces_no20 bray data..."## Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`.
## ℹ See also `vignette("ggplot2-in-packages")` for more information.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## $sites
## PCoA1 PCoA2
## c1_F0R04 -0.221345663 -0.336827578
## c1_F0R06 -0.254521464 0.047173488
## c1_F0R07 -0.146568426 -0.469015246
## c1_F0R08 -0.262213150 -0.010219927
## c1_F0R09 -0.233485209 0.142965549
## c1_F0R12 -0.260201883 -0.207729595
## c1_F0R14 -0.214437318 -0.261957632
## c1_F0R15 -0.269088631 -0.199411592
## c1_F0R24 -0.250109012 -0.065543553
## c1_F0R28 0.098777294 -0.019304023
## c1_F0R30 0.497058432 0.005742187
## c1_F0R33 0.167471022 -0.367254960
## c1_F0R35 0.474091679 0.082893522
## c1_F0R36 0.523890094 0.068879307
## c1_F0R38 0.392388883 0.074491067
## c1_F0R40 0.176118554 -0.074996844
## c1_F0R42 0.522236568 0.094488366
## c1_F0R44 0.320927566 -0.211097753
## c1_F0R45 0.505828418 0.086121728
## c1_F0R47 0.454264755 0.071747833
## c1_F12R09 -0.272141028 -0.134673138
## c1_F12R19 -0.245059744 0.213736632
## c1_F12R33 -0.042952171 -0.414357246
## c1_F12R42 0.470657876 0.102010370
## c1_F16R08 -0.220239466 -0.200982135
## c1_F16R20 -0.254406479 -0.039715040
## c1_F16R21 -0.240942991 -0.172001682
## c1_F16R22 -0.305062119 -0.068743116
## c1_F16R33 -0.094686597 -0.548070210
## c1_F16R36 0.380017427 -0.137886911
## c1_F21R19 -0.304468462 0.170640507
## c1_F21R23 -0.296608394 0.086314623
## c1_F21R34 0.342915825 -0.004636889
## c1_F21R42 0.348673021 0.059401464
## c1_F21R46 0.508787794 0.130680638
## c1_F8R09 -0.315499354 0.139179993
## c1_F8R12 -0.271593468 -0.235188640
## c1_F8R17 -0.240004240 -0.018886626
## c1_F8R18 -0.327681353 0.128056910
## c1_F8R22 -0.290543128 0.026645199
## c1_F8R29 0.496477946 0.045217659
## c1_F8R34 0.416972122 0.067932603
## c1_F8R36 0.346614303 0.004905345
## c1_F8R39 0.135953607 -0.224651949
## c1_F8R40 0.377328680 0.125011582
## c1_F8R46 0.445080223 0.142868152
## c1_F8R48 0.351212339 0.056086563
## c2_F0R01 -0.261792668 -0.137939176
## c2_F0R05 -0.261679642 -0.199810214
## c2_F0R13 -0.280542141 0.020890452
## c2_F0R17 -0.191387787 -0.186449182
## c2_F0R18 -0.252498338 -0.181270038
## c2_F0R19 -0.297217650 0.045902731
## c2_F0R20 -0.276737308 0.091629418
## c2_F0R25 0.342137422 0.051182653
## c2_F0R29 0.494727578 0.069476075
## c2_F0R34 0.441139835 0.062287149
## c2_F0R37 0.235702906 -0.170835571
## c2_F0R39 0.315660769 -0.096473464
## c2_F0R43 0.384933340 0.092276711
## c2_F0R48 0.322886741 -0.046807829
## c2_F12R07 -0.325705950 0.100551697
## c2_F12R23 -0.218239006 0.199223408
## c2_F12R31 0.441151809 0.043266311
## c2_F12R45 0.249417866 -0.073431244
## c2_F12R47 -0.065818605 -0.329645418
## c2_F16R19 -0.292512152 0.258217351
## c2_F16R42 0.352903874 0.051064373
## c2_F16R45 0.045240650 -0.209919327
## c2_F16R48 0.489409547 0.090433076
## c2_F21R10 -0.229709790 -0.004511956
## c2_F21R20 -0.275777516 0.148360279
## c2_F21R21 -0.239631663 0.068786730
## c2_F21R24 -0.302931686 0.276893388
## c2_F21R36 -0.019632451 -0.215938062
## c2_F8R02 -0.307030480 0.054985160
## c2_F8R16 -0.273253410 0.257979596
## c2_F8R20 -0.278505776 0.018929663
## c2_F8R31 0.497233012 0.109137989
## c2_F8R35 0.501040605 0.142312092
## c2_F8R41 0.340861812 0.109233370
## c2_F8R42 0.129628979 0.021612847
## c2_F8R43 -0.171920046 0.002178168
## c2_F8R44 -0.191243870 -0.017393756
## c2_F8R47 0.064631200 -0.079984181
## c3_F0R16 -0.287242815 0.254329397
## c3_F0R21 -0.272874916 -0.081506216
## c3_F0R23 -0.276637030 0.144519575
## c3_F0R26 0.406350543 -0.048467532
## c3_F0R41 0.518756213 0.123265585
## c3_F12R08 -0.234961008 -0.196786277
## c3_F12R10 -0.289626280 0.132167103
## c3_F12R11 -0.290966322 0.114616268
## c3_F12R20 -0.292503042 0.292303312
## c3_F12R21 -0.264003389 0.111872710
## c3_F12R22 -0.294931776 0.092230453
## c3_F12R32 0.001649408 -0.146130829
## c3_F16R07 -0.334617599 -0.034262622
## c3_F16R11 -0.296213286 -0.048158131
## c3_F16R12 -0.296212380 -0.009502628
## c3_F16R23 -0.303441903 0.239995649
## c3_F16R31 0.388961357 -0.043214199
## c3_F16R32 0.354052133 0.015824041
## c3_F16R34 0.049344361 -0.304256108
## c3_F16R47 0.046392773 -0.326790477
## c3_F21R09 -0.275114852 -0.036790113
## c3_F21R12 -0.271399573 0.249441293
## c3_F21R22 -0.302931522 0.203787326
## c3_F21R31 0.423688521 0.026420869
## c3_F21R35 0.450596450 0.111324672
## c3_F21R45 -0.208037754 -0.256256416
## c3_F21R47 -0.154563903 -0.100143893
## c3_F8R04 -0.234921035 0.037038012
## c3_F8R06 -0.220090827 0.152851957
## c3_F8R07 -0.325078782 -0.035882688
## c3_F8R10 -0.313207734 0.019234558
## c3_F8R11 -0.301302693 0.154052484
## c3_F8R13 -0.320877278 0.155488009
## c3_F8R14 -0.287749901 0.242131281
## c3_F8R19 -0.294767159 0.214614685
## c3_F8R23 -0.289170117 0.273979320
## c3_F8R24 -0.319350250 0.109513818
## c3_F8R26 0.447284972 0.058209248
## c3_F8R27 0.264706806 0.104203685
## c3_F8R32 -0.040537038 0.006348014
## c3_F8R38 -0.153562446 -0.223403878
## c3_F8R45 0.019498626 -0.085004565
## c4_F0R02 -0.292949724 0.117954495
## c4_F0R03 -0.240737525 -0.097473156
## c4_F0R10 -0.190840802 -0.322532523
## c4_F0R11 -0.273164910 -0.124037917
## c4_F0R22 -0.269295362 -0.020308083
## c4_F0R27 0.439011977 -0.030059973
## c4_F0R31 0.423699875 0.007056778
## c4_F0R32 0.422228776 0.059931070
## c4_F0R46 0.523499750 0.122284141
## c4_F12R12 -0.313659403 0.128860644
## c4_F12R24 -0.281557077 0.207976241
## c4_F12R34 0.286587124 -0.096639480
## c4_F12R35 0.455690893 -0.004062885
## c4_F12R36 0.266121663 -0.006069061
## c4_F12R41 0.263503511 0.019478418
## c4_F12R46 0.340160921 -0.001142570
## c4_F12R48 0.480921060 0.109150292
## c4_F16R09 -0.296335555 0.135093812
## c4_F16R10 -0.281777882 0.018304242
## c4_F16R24 -0.283406151 0.101510097
## c4_F16R35 0.525372202 0.105832180
## c4_F16R41 0.336988030 0.042277616
## c4_F16R46 0.402272360 0.006701014
## c4_F21R07 -0.243478899 -0.141663270
## c4_F21R08 -0.181215017 -0.198896612
## c4_F21R11 -0.231806579 0.191916738
## c4_F21R32 0.054005803 -0.088035580
## c4_F21R33 -0.069270606 -0.336507244
## c4_F21R41 0.253979269 -0.010041653
## c4_F21R48 0.418605953 0.045495330
## c4_F8R01 -0.298891981 0.277228486
## c4_F8R03 -0.289293566 0.215168107
## c4_F8R05 -0.224396754 0.082484581
## c4_F8R08 -0.271518299 -0.077901093
## c4_F8R15 -0.301177906 0.205421972
## c4_F8R21 -0.251896802 0.023314408
## c4_F8R25 0.231295911 -0.112167356
## c4_F8R28 -0.141080224 0.025786460
## c4_F8R30 0.289184835 -0.072367228
## c4_F8R33 0.085476328 -0.207301024
## c4_F8R37 -0.150067464 -0.151667437
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL 0.4223232 0.016440776
## 0_HF_PFOS 0.4103575 0.026219360
## 0_LF_CTRL -0.2446940 -0.143766715
## 0_LF_PFOS -0.2627842 -0.036571970
## 12_HF_CTRL 0.2942247 -0.063123927
## 12_HF_PFOS 0.3212897 -0.005226642
## 12_LF_CTRL -0.2949107 0.050935289
## 12_LF_PFOS -0.2664796 0.184096234
## 16_HF_CTRL 0.3224563 -0.099946001
## 16_HF_PFOS 0.3178762 -0.017303053
## 16_LF_CTRL -0.2958864 -0.018233610
## 16_LF_PFOS -0.2813465 0.053159535
## 21_HF_CTRL 0.2178320 -0.070287971
## 21_HF_PFOS 0.2506034 0.002296517
## 21_LF_CTRL -0.2416181 -0.003889425
## 21_LF_PFOS -0.2889142 0.164367867
## 8_HF_CTRL 0.3313533 0.025801383
## 8_HF_PFOS 0.1024838 -0.030260707
## 8_LF_CTRL -0.2847390 0.069786285
## 8_LF_PFOS -0.2928641 0.144049535
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 19 0.26838 0.014125 1.1307 0.3266
## Residuals 148 1.84891 0.012493## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 1.844 0.04572 3.0500 0.001 ***
## feed 1 12.871 0.31922 85.1749 0.001 ***
## PFOS 1 0.411 0.01020 2.7225 0.015 *
## day:feed 4 1.482 0.03676 2.4521 0.001 ***
## day:PFOS 3 0.380 0.00942 0.8379 0.608
## feed:PFOS 1 0.269 0.00668 1.7825 0.107
## day:feed:PFOS 3 0.396 0.00981 0.8726 0.570
## Residual 150 22.668 0.56218
## Total 167 40.321 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Feces_no20 jac data..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 -0.168294198 -0.213488011
## c1_F0R06 -0.041505797 -0.290729632
## c1_F0R07 -0.188234633 -0.195022540
## c1_F0R08 -0.114755752 -0.242035336
## c1_F0R09 -0.096582255 -0.262617803
## c1_F0R12 -0.129534635 -0.233222082
## c1_F0R14 -0.125195338 -0.255435017
## c1_F0R15 -0.088889172 -0.279047673
## c1_F0R24 -0.077233372 -0.274613209
## c1_F0R28 -0.210873652 -0.194058458
## c1_F0R30 -0.369205637 -0.027811301
## c1_F0R33 -0.241460941 -0.142295673
## c1_F0R35 -0.224900493 -0.145171366
## c1_F0R36 -0.361157785 0.005107767
## c1_F0R38 -0.224916635 -0.144030800
## c1_F0R40 -0.152482670 -0.214166829
## c1_F0R42 -0.364472058 -0.025557949
## c1_F0R44 -0.323730743 -0.086177904
## c1_F0R45 -0.386651156 0.017031830
## c1_F0R47 -0.174590773 -0.164857795
## c1_F12R09 -0.054077972 -0.274295102
## c1_F12R19 -0.026551766 -0.309439095
## c1_F12R33 -0.200430558 -0.142505987
## c1_F12R42 -0.341521048 -0.039363434
## c1_F16R08 -0.042054412 -0.281694566
## c1_F16R20 -0.067978810 -0.265687565
## c1_F16R21 -0.059979747 -0.282215313
## c1_F16R22 -0.023646128 -0.306427097
## c1_F16R33 -0.190671644 -0.172534335
## c1_F16R36 -0.215044050 -0.145904771
## c1_F21R19 -0.016544071 -0.311273223
## c1_F21R23 -0.035104792 -0.296340644
## c1_F21R34 -0.205114981 -0.174255812
## c1_F21R42 -0.227829921 -0.153561201
## c1_F21R46 -0.373042612 0.011726370
## c1_F8R09 -0.057076506 -0.300234908
## c1_F8R12 -0.089944696 -0.267428068
## c1_F8R17 -0.107745549 -0.236051864
## c1_F8R18 -0.063860165 -0.269135523
## c1_F8R22 -0.100033466 -0.256037224
## c1_F8R29 -0.327849361 -0.036115587
## c1_F8R34 -0.298380883 -0.096116285
## c1_F8R36 -0.284959173 -0.086584168
## c1_F8R39 -0.196153448 -0.174347909
## c1_F8R40 -0.163171114 -0.213569249
## c1_F8R46 -0.345718087 -0.043021392
## c1_F8R48 -0.313011877 -0.071761995
## c2_F0R01 0.101884268 -0.017402848
## c2_F0R05 0.128346121 -0.030167053
## c2_F0R13 0.112631748 -0.005068533
## c2_F0R17 0.073041567 0.016656880
## c2_F0R18 0.132852249 -0.027156209
## c2_F0R19 0.120161680 -0.042594813
## c2_F0R20 0.116834680 -0.019697637
## c2_F0R25 0.027384270 0.029869320
## c2_F0R29 -0.162430017 0.229127178
## c2_F0R34 -0.170474794 0.186195638
## c2_F0R37 -0.046993293 0.040142331
## c2_F0R39 -0.084003048 0.118200185
## c2_F0R43 -0.004485274 0.023042364
## c2_F0R48 -0.149811198 0.232547536
## c2_F12R07 0.162748839 -0.061959755
## c2_F12R23 0.146894294 -0.046311609
## c2_F12R31 -0.206697120 0.229819032
## c2_F12R45 0.015410638 0.045941175
## c2_F12R47 0.078156429 0.042168323
## c2_F16R19 0.174166139 -0.097921894
## c2_F16R42 -0.060073840 0.081147762
## c2_F16R45 0.059572135 0.021528966
## c2_F16R48 -0.216743602 0.192850205
## c2_F21R10 0.149407849 -0.054266060
## c2_F21R20 0.161427340 -0.061783435
## c2_F21R21 0.199749913 -0.051909635
## c2_F21R24 0.193734880 -0.078777397
## c2_F21R36 0.005932272 0.065314626
## c2_F8R02 0.173259149 -0.058168253
## c2_F8R16 0.141907608 -0.084145066
## c2_F8R20 0.134595475 -0.056840492
## c2_F8R31 -0.170811052 0.213400577
## c2_F8R35 -0.260517280 0.216039306
## c2_F8R41 -0.097772912 0.121307877
## c2_F8R42 -0.114294251 0.156591280
## c2_F8R43 0.062006877 -0.036045664
## c2_F8R44 0.075824332 -0.013444866
## c2_F8R47 0.015900270 0.055445642
## c3_F0R16 0.219565628 -0.030659941
## c3_F0R21 0.203516419 0.026649638
## c3_F0R23 0.181719176 0.041688623
## c3_F0R26 -0.144776697 0.211153412
## c3_F0R41 -0.159532215 0.231073153
## c3_F12R08 0.225336049 -0.052214013
## c3_F12R10 0.238023639 -0.021314674
## c3_F12R11 0.280363501 -0.057787741
## c3_F12R20 0.202163343 -0.003483668
## c3_F12R21 0.225229988 0.008128601
## c3_F12R22 0.259579292 -0.015156114
## c3_F12R32 0.055716059 0.109410512
## c3_F16R07 0.248689278 -0.013719990
## c3_F16R11 0.236214362 -0.024666197
## c3_F16R12 0.228606605 -0.030512046
## c3_F16R23 0.258705817 -0.037149073
## c3_F16R31 -0.115427399 0.205756910
## c3_F16R32 0.008749647 0.151961672
## c3_F16R34 -0.036751721 0.189046037
## c3_F16R47 0.066243511 0.082370024
## c3_F21R09 0.226387883 -0.013642486
## c3_F21R12 0.226001467 -0.044605991
## c3_F21R22 0.283335066 -0.023231442
## c3_F21R31 -0.150340008 0.249247188
## c3_F21R35 -0.119844576 0.216920139
## c3_F21R45 0.173224298 0.074848888
## c3_F21R47 0.152071211 0.028719993
## c3_F8R04 0.191281860 0.030308100
## c3_F8R06 0.233891042 -0.039341550
## c3_F8R07 0.222721439 0.005543436
## c3_F8R10 0.214126408 -0.007523088
## c3_F8R11 0.271666636 -0.030018606
## c3_F8R13 0.215356624 0.008390157
## c3_F8R14 0.223656001 -0.028187604
## c3_F8R19 0.243404128 -0.003833806
## c3_F8R23 0.173840272 0.011861494
## c3_F8R24 0.237523392 -0.011852410
## c3_F8R26 -0.128043102 0.209499659
## c3_F8R27 -0.042779275 0.227838304
## c3_F8R32 0.046685685 0.134074934
## c3_F8R38 0.131608192 0.082922885
## c3_F8R45 0.089139358 0.119364365
## c4_F0R02 0.105819088 0.041298752
## c4_F0R03 0.052495532 0.103101639
## c4_F0R10 0.060868365 0.116383530
## c4_F0R11 0.148920398 0.069729175
## c4_F0R22 0.163031861 0.058753055
## c4_F0R27 -0.101068771 0.228636844
## c4_F0R31 -0.130057777 0.229578519
## c4_F0R32 -0.040232728 0.187198391
## c4_F0R46 -0.213517983 0.246504928
## c4_F12R12 0.167465067 0.017549771
## c4_F12R24 0.201987031 -0.025482121
## c4_F12R34 -0.118468551 0.229351005
## c4_F12R35 -0.152398587 0.236831889
## c4_F12R36 -0.094019645 0.194818847
## c4_F12R41 0.006905068 0.111119222
## c4_F12R46 -0.150069132 0.269490581
## c4_F12R48 -0.188992506 0.253045292
## c4_F16R09 0.211616385 -0.002582679
## c4_F16R10 0.229116738 0.002634330
## c4_F16R24 0.234843246 -0.006894824
## c4_F16R35 -0.180679267 0.254613713
## c4_F16R41 -0.024835371 0.175069242
## c4_F16R46 -0.134947871 0.253176206
## c4_F21R07 0.229449191 0.003234492
## c4_F21R08 0.199648422 -0.001850205
## c4_F21R11 0.244995526 -0.015464406
## c4_F21R32 0.004317806 0.168081209
## c4_F21R33 0.029111260 0.130362854
## c4_F21R41 -0.001913752 0.175909485
## c4_F21R48 -0.187779978 0.282908614
## c4_F8R01 0.162427118 0.025789744
## c4_F8R03 0.144139706 0.038003639
## c4_F8R05 0.173853820 0.065863654
## c4_F8R08 0.172266565 0.040870880
## c4_F8R15 0.184431967 0.026126311
## c4_F8R21 0.163756714 0.056429654
## c4_F8R25 0.050004411 0.105509004
## c4_F8R28 0.034404517 0.087630581
## c4_F8R30 -0.111428365 0.247355993
## c4_F8R33 0.032436286 0.132269117
## c4_F8R37 0.098691108 0.107867133
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL -0.17798566 0.071356725
## 0_HF_PFOS -0.19580108 0.013726443
## 0_LF_CTRL -0.02002756 -0.108110863
## 0_LF_PFOS 0.09149003 -0.056309376
## 12_HF_CTRL -0.12150786 0.160522265
## 12_HF_PFOS -0.09634838 0.121866899
## 12_LF_CTRL 0.18489479 -0.067377871
## 12_LF_PFOS 0.17731502 -0.054658373
## 16_HF_CTRL -0.11559200 0.086764405
## 16_HF_PFOS -0.05116676 0.129523748
## 16_LF_CTRL 0.19663413 -0.048637423
## 16_LF_PFOS 0.06816477 -0.182285094
## 21_HF_CTRL -0.06682471 0.114828987
## 21_HF_PFOS -0.06929750 0.072544397
## 21_LF_CTRL 0.21378148 -0.018661927
## 21_LF_PFOS 0.13596726 -0.129829368
## 8_HF_CTRL -0.12550473 0.112564309
## 8_HF_PFOS -0.05646368 0.008586226
## 8_LF_CTRL 0.16106366 -0.031785454
## 8_LF_PFOS 0.13209968 -0.061845003
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 19 0.10281 0.0054112 2.6217 0.0006192 ***
## Residuals 148 0.30547 0.0020640
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 1.3661 0.04453 2.1805 0.001 ***
## feed 1 3.6810 0.12000 23.5014 0.001 ***
## PFOS 1 0.3109 0.01013 1.9848 0.016 *
## day:feed 4 0.8399 0.02738 1.3405 0.046 *
## day:PFOS 3 0.3189 0.01040 0.6788 0.985
## feed:PFOS 1 0.2990 0.00975 1.9092 0.024 *
## day:feed:PFOS 3 0.3654 0.01191 0.7777 0.885
## Residual 150 23.4941 0.76590
## Total 167 30.6752 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Feces_no20 unif data..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 -0.105591581 -8.835997e-02
## c1_F0R06 0.028862692 -1.656222e-01
## c1_F0R07 -0.049808226 -1.381016e-01
## c1_F0R08 -0.014808767 -1.248571e-01
## c1_F0R09 -0.008475157 -1.483880e-01
## c1_F0R12 -0.027271659 -8.922844e-02
## c1_F0R14 0.012364390 -1.434252e-01
## c1_F0R15 0.009955890 -1.476676e-01
## c1_F0R24 0.024716018 -1.575667e-01
## c1_F0R28 -0.066716031 -1.624876e-01
## c1_F0R30 -0.241853426 -9.104576e-02
## c1_F0R33 -0.106466965 -1.358934e-01
## c1_F0R35 -0.047308515 -1.920900e-01
## c1_F0R36 -0.267896192 -4.608769e-02
## c1_F0R38 -0.097943937 -1.574740e-01
## c1_F0R40 -0.066888377 -1.578423e-01
## c1_F0R42 -0.230238812 -7.398735e-02
## c1_F0R44 -0.182121342 -8.968396e-02
## c1_F0R45 -0.256867462 -3.555329e-02
## c1_F0R47 -0.113690701 -1.445316e-01
## c1_F12R09 0.002949722 -1.432694e-01
## c1_F12R19 0.061766863 -1.565117e-01
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## c1_F16R08 0.047343051 -1.735457e-01
## c1_F16R20 0.003175506 -1.113702e-01
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## c1_F16R22 0.071943991 -1.664337e-01
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## c1_F8R09 0.037101858 -1.516795e-01
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## c2_F0R01 0.112057465 1.777829e-02
## c2_F0R05 0.119602122 9.150254e-03
## c2_F0R13 0.044892086 2.589782e-02
## c2_F0R17 0.050031276 4.740103e-02
## c2_F0R18 0.113144634 3.450680e-03
## c2_F0R19 0.100714672 -1.745843e-02
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## c2_F12R47 0.024361657 1.040720e-02
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## c2_F21R20 0.134264863 -1.713146e-03
## c2_F21R21 0.181186582 1.171644e-02
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## c2_F21R36 0.003409374 1.343258e-04
## c2_F8R02 0.134945762 1.321463e-02
## c2_F8R16 0.134201416 -1.665964e-02
## c2_F8R20 0.112611979 -8.145294e-03
## c2_F8R31 -0.171569897 8.080780e-02
## c2_F8R35 -0.211853717 5.589328e-02
## c2_F8R41 -0.060971193 4.487259e-02
## c2_F8R42 -0.087951847 9.976540e-02
## c2_F8R43 0.057193706 -3.973157e-02
## c2_F8R44 0.064590195 -1.140767e-02
## c2_F8R47 -0.001654479 4.098620e-02
## c3_F0R16 0.105508863 -1.187067e-02
## c3_F0R21 0.069506671 4.574126e-02
## c3_F0R23 0.072128763 3.250909e-02
## c3_F0R26 -0.241772780 6.841395e-02
## c3_F0R41 -0.206526201 6.347235e-02
## c3_F12R08 0.128997045 7.966010e-03
## c3_F12R10 0.130101084 -3.100217e-03
## c3_F12R11 0.178456374 1.385807e-03
## c3_F12R20 0.063186958 1.973290e-02
## c3_F12R21 0.124055694 3.894218e-02
## c3_F12R22 0.119413350 1.153181e-02
## c3_F12R32 -0.003303566 -1.207744e-02
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## c3_F16R23 0.141702095 1.633095e-02
## c3_F16R31 -0.198327170 8.539179e-02
## c3_F16R32 -0.086151130 4.238329e-02
## c3_F16R34 -0.102162118 8.845355e-02
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## c3_F21R09 0.137895127 -1.045249e-02
## c3_F21R12 0.092935729 1.017003e-03
## c3_F21R22 0.171738622 -1.458898e-02
## c3_F21R31 -0.221677975 8.169140e-02
## c3_F21R35 -0.180763223 1.067145e-01
## c3_F21R45 0.079504468 4.428604e-02
## c3_F21R47 0.062760929 -1.683694e-02
## c3_F8R04 0.069660946 5.764008e-02
## c3_F8R06 0.143855277 -3.033787e-02
## c3_F8R07 0.098527116 3.738810e-02
## c3_F8R10 0.082006353 1.561026e-02
## c3_F8R11 0.164131617 3.280176e-02
## c3_F8R13 0.092800789 4.917076e-02
## c3_F8R14 0.115525859 -1.606722e-03
## c3_F8R19 0.117419631 5.073317e-02
## c3_F8R23 0.052416127 4.541910e-02
## c3_F8R24 0.098927041 4.022502e-02
## c3_F8R26 -0.173370473 9.311915e-02
## c3_F8R27 -0.163653813 1.408236e-01
## c3_F8R32 -0.026904152 2.712152e-02
## c3_F8R38 0.054618672 3.092241e-02
## c3_F8R45 0.028395882 6.306147e-02
## c4_F0R02 0.072140780 1.045029e-01
## c4_F0R03 -0.019446510 1.332392e-01
## c4_F0R10 0.058490040 8.204745e-02
## c4_F0R11 0.094614948 7.062071e-02
## c4_F0R22 0.107483142 6.354279e-02
## c4_F0R27 -0.103953360 1.230451e-01
## c4_F0R31 -0.175292899 1.373181e-01
## c4_F0R32 -0.036001945 9.192977e-02
## c4_F0R46 -0.204397418 1.168619e-01
## c4_F12R12 0.158501462 6.087883e-02
## c4_F12R24 0.167644123 5.960287e-02
## c4_F12R34 -0.127075419 1.523831e-01
## c4_F12R35 -0.148339353 1.240353e-01
## c4_F12R36 -0.063846602 9.568884e-02
## c4_F12R41 -0.010923866 3.209699e-02
## c4_F12R46 -0.136428497 1.273843e-01
## c4_F12R48 -0.148475840 1.217185e-01
## c4_F16R09 0.197261791 4.095079e-02
## c4_F16R10 0.199768690 4.212317e-02
## c4_F16R24 0.194277540 6.106379e-02
## c4_F16R35 -0.174207912 9.566434e-02
## c4_F16R41 -0.028031403 8.072221e-02
## c4_F16R46 -0.104273531 1.312534e-01
## c4_F21R07 0.192366462 5.797131e-02
## c4_F21R08 0.169626515 3.725251e-02
## c4_F21R11 0.216321307 7.475125e-02
## c4_F21R32 -0.028660119 1.424276e-01
## c4_F21R33 0.015107066 8.521228e-02
## c4_F21R41 0.006493511 8.805951e-02
## c4_F21R48 -0.177450980 1.396822e-01
## c4_F8R01 0.176446889 7.124685e-02
## c4_F8R03 0.085972760 8.236763e-02
## c4_F8R05 0.098368415 1.186583e-01
## c4_F8R08 0.102438189 8.997696e-02
## c4_F8R15 0.139728576 1.052751e-01
## c4_F8R21 0.118920798 1.109046e-01
## c4_F8R25 0.062519931 1.917900e-02
## c4_F8R28 0.036690386 1.877869e-02
## c4_F8R30 -0.127824973 1.372068e-01
## c4_F8R33 0.027982230 5.583169e-02
## c4_F8R37 0.081132359 8.156480e-02
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL -0.13486330 -0.003667486
## 0_HF_PFOS -0.14057036 -0.046209019
## 0_LF_CTRL 0.02295731 -0.033315095
## 0_LF_PFOS 0.06573848 -0.011878817
## 12_HF_CTRL -0.10535050 0.060394253
## 12_HF_PFOS -0.07839991 0.046958231
## 12_LF_CTRL 0.12740842 -0.005381579
## 12_LF_PFOS 0.11143024 0.003086605
## 16_HF_CTRL -0.12688429 0.014275865
## 16_HF_PFOS -0.04017946 0.043231497
## 16_LF_CTRL 0.15821954 -0.010012457
## 16_LF_PFOS 0.10678677 -0.063072543
## 21_HF_CTRL -0.07923042 0.050817142
## 21_HF_PFOS -0.04029919 0.011587190
## 21_LF_CTRL 0.15897252 0.024780344
## 21_LF_PFOS 0.13253391 -0.050492558
## 8_HF_CTRL -0.11074388 0.030628579
## 8_HF_PFOS -0.02734800 -0.003351205
## 8_LF_CTRL 0.10416147 0.022305323
## 8_LF_PFOS 0.08252013 0.005149952
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 19 0.083225 0.0043803 4.8914 8.824e-09 ***
## Residuals 148 0.132535 0.0008955
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 0.5756 0.05332 2.7778 0.001 ***
## feed 1 1.7092 0.15832 32.9921 0.001 ***
## PFOS 1 0.0749 0.00694 1.4460 0.125
## day:feed 4 0.3017 0.02795 1.4559 0.041 *
## day:PFOS 3 0.1091 0.01011 0.7023 0.943
## feed:PFOS 1 0.1200 0.01111 2.3154 0.010 **
## day:feed:PFOS 3 0.1344 0.01245 0.8649 0.666
## Residual 150 7.7710 0.71980
## Total 167 10.7960 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Feces_no20 wuf data..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 0.293331595 -0.2905905947
## c1_F0R06 -0.094054011 0.0259808482
## c1_F0R07 0.312214662 -0.4071273771
## c1_F0R08 -0.147115726 -0.0776776132
## c1_F0R09 -0.221155672 0.0372838453
## c1_F0R12 0.225127913 -0.1928649877
## c1_F0R14 0.225621630 -0.2474114232
## c1_F0R15 0.245588542 -0.1358089622
## c1_F0R24 -0.065970742 -0.1544610150
## c1_F0R28 -0.184403071 -0.0052816735
## c1_F0R30 -0.317581637 -0.0845454599
## c1_F0R33 0.044610783 -0.2863834709
## c1_F0R35 -0.428033071 -0.0564421277
## c1_F0R36 -0.448002169 -0.0983713559
## c1_F0R38 -0.375161897 -0.0344111033
## c1_F0R40 -0.171040071 -0.0468502607
## c1_F0R42 -0.497272984 -0.0920460731
## c1_F0R44 -0.124300801 -0.1976394072
## c1_F0R45 -0.480015582 -0.0872929109
## c1_F0R47 -0.376902930 -0.0481114057
## c1_F12R09 0.307814170 -0.1231106150
## c1_F12R19 -0.206745127 0.0273746154
## c1_F12R33 0.300348371 -0.3860009421
## c1_F12R42 -0.448181457 -0.0747680141
## c1_F16R08 0.285911731 -0.0849103820
## c1_F16R20 0.169742009 0.0550082126
## c1_F16R21 0.296426821 -0.1646412156
## c1_F16R22 0.187751441 -0.0314558510
## c1_F16R33 0.331558818 -0.4280344571
## c1_F16R36 -0.200589337 -0.2248312348
## c1_F21R19 -0.096406749 0.0588377534
## c1_F21R23 0.161109409 0.0101790484
## c1_F21R34 -0.203612099 -0.0015357160
## c1_F21R42 -0.303196952 -0.0413937918
## c1_F21R46 -0.473381356 -0.0587970515
## c1_F8R09 -0.040824382 0.0750222431
## c1_F8R12 0.292425982 -0.2325175768
## c1_F8R17 0.280583033 -0.0425763825
## c1_F8R18 -0.045938611 0.0568775377
## c1_F8R22 -0.109267610 -0.0508101651
## c1_F8R29 -0.389161295 -0.0910103841
## c1_F8R34 -0.367763285 -0.0754684415
## c1_F8R36 -0.238899393 -0.0206133290
## c1_F8R39 -0.014626497 -0.2220151217
## c1_F8R40 -0.383487569 -0.0806095626
## c1_F8R46 -0.403292923 -0.0401782096
## c1_F8R48 -0.251414670 -0.0717752860
## c2_F0R01 0.197864013 -0.1258768781
## c2_F0R05 0.281779370 -0.1127749836
## c2_F0R13 0.082632012 0.0507910176
## c2_F0R17 0.261040580 -0.1914779880
## c2_F0R18 0.118276141 -0.1082894825
## c2_F0R19 -0.116017128 0.0049930342
## c2_F0R20 -0.006502103 0.1060455203
## c2_F0R25 -0.245192657 -0.0729383487
## c2_F0R29 -0.260939556 0.0274357073
## c2_F0R34 -0.343751335 -0.0201979148
## c2_F0R37 -0.121854974 -0.0838032147
## c2_F0R39 -0.180856264 -0.1354193008
## c2_F0R43 -0.372513228 -0.0276586140
## c2_F0R48 -0.040112383 0.0732312318
## c2_F12R07 0.115083688 0.0416993990
## c2_F12R23 0.142324070 0.1327520967
## c2_F12R31 -0.189831771 0.0505313671
## c2_F12R45 -0.101980951 -0.0524100190
## c2_F12R47 0.315854141 -0.2725649772
## c2_F16R19 -0.087002519 0.1686749198
## c2_F16R42 -0.158832106 0.0749554290
## c2_F16R45 0.041051158 -0.1194865804
## c2_F16R48 -0.333595998 -0.0040044953
## c2_F21R10 0.139826922 -0.0112317600
## c2_F21R20 0.203081658 0.1349233583
## c2_F21R21 0.223512816 0.1701481641
## c2_F21R24 0.032708338 0.1739796559
## c2_F21R36 0.112525615 -0.0227512236
## c2_F8R02 0.170435245 0.1028974626
## c2_F8R16 -0.121035020 0.1411425726
## c2_F8R20 0.213208953 0.0448455993
## c2_F8R31 -0.454745498 -0.0527103515
## c2_F8R35 -0.478816529 -0.0502862448
## c2_F8R41 -0.281912857 0.0839602398
## c2_F8R42 0.077835517 0.1426206329
## c2_F8R43 -0.130074570 -0.0179646904
## c2_F8R44 -0.084892414 -0.0053889124
## c2_F8R47 -0.045376022 -0.0502053742
## c3_F0R16 -0.120539891 0.1086283100
## c3_F0R21 0.348391794 0.0778685726
## c3_F0R23 0.137423120 0.1863897767
## c3_F0R26 -0.106864039 -0.0688243189
## c3_F0R41 -0.405096492 0.0088703261
## c3_F12R08 0.303797367 -0.0997977700
## c3_F12R10 0.129921004 0.1590165109
## c3_F12R11 0.170382297 0.1227283463
## c3_F12R20 -0.157343725 0.1278639271
## c3_F12R21 0.272015389 0.1835902756
## c3_F12R22 0.253927980 0.1586367860
## c3_F12R32 0.064225601 -0.0012660641
## c3_F16R07 0.261550025 -0.0153925379
## c3_F16R11 0.264922521 -0.0285679247
## c3_F16R12 0.351587377 0.0002775919
## c3_F16R23 0.188509656 0.1846956307
## c3_F16R31 -0.186915027 -0.0816924431
## c3_F16R32 -0.302445309 -0.0183277634
## c3_F16R34 0.214018704 -0.0624154311
## c3_F16R47 0.172280885 -0.2371394474
## c3_F21R09 0.261433727 0.0113666036
## c3_F21R12 0.012524799 0.0999222265
## c3_F21R22 0.167986634 0.2055694526
## c3_F21R31 -0.224981653 0.0112628661
## c3_F21R35 -0.224626299 0.0990134310
## c3_F21R45 0.225440753 -0.0771636654
## c3_F21R47 0.173440969 0.0127159447
## c3_F8R04 0.278141351 0.1471794686
## c3_F8R06 0.061492598 0.0730834082
## c3_F8R07 0.352793268 0.0383252641
## c3_F8R10 0.246115482 0.0656497205
## c3_F8R11 0.191936947 0.1212692026
## c3_F8R13 0.130485229 0.1677110005
## c3_F8R14 0.044152808 0.1699693890
## c3_F8R19 0.172447735 0.1921408070
## c3_F8R23 0.158532830 0.2385560197
## c3_F8R24 0.070110725 0.1047479208
## c3_F8R26 -0.274018226 0.0084813098
## c3_F8R27 -0.097853059 0.1568499550
## c3_F8R32 -0.018616707 0.0969940453
## c3_F8R38 0.265439652 -0.0276597063
## c3_F8R45 0.077959294 0.0644847056
## c4_F0R02 0.205898289 0.1346680409
## c4_F0R03 0.263689783 -0.0223323119
## c4_F0R10 0.329092957 -0.2175743021
## c4_F0R11 0.059556365 -0.1349944793
## c4_F0R22 0.271267525 0.0824893111
## c4_F0R27 -0.168210407 0.0277735611
## c4_F0R31 -0.221236371 0.0343895514
## c4_F0R32 -0.325652490 -0.0098276759
## c4_F0R46 -0.388354374 0.0071161758
## c4_F12R12 0.207717004 0.1094354500
## c4_F12R24 0.139679905 0.1414630239
## c4_F12R34 0.005700794 0.0355373737
## c4_F12R35 -0.122583101 0.0480312372
## c4_F12R36 0.014261269 0.1056045220
## c4_F12R41 -0.055245042 0.1829650303
## c4_F12R46 -0.020191978 0.0990010601
## c4_F12R48 -0.345417982 -0.0067860671
## c4_F16R09 0.149616012 0.1366239664
## c4_F16R10 0.277712564 0.0931586335
## c4_F16R24 0.292051597 0.1134311184
## c4_F16R35 -0.372791783 -0.0125044014
## c4_F16R41 -0.247678442 0.0605276755
## c4_F16R46 -0.074476017 0.1040945800
## c4_F21R07 0.298975781 -0.1031959221
## c4_F21R08 0.346484539 -0.1613606737
## c4_F21R11 0.257802765 0.2072635786
## c4_F21R32 0.011959901 0.0197760592
## c4_F21R33 0.294153718 -0.1200734045
## c4_F21R41 -0.213201778 0.0473307965
## c4_F21R48 -0.106797357 0.1021490033
## c4_F8R01 -0.175463047 0.1194553078
## c4_F8R03 0.075639801 0.1388618524
## c4_F8R05 0.259330728 0.0987434887
## c4_F8R08 0.046729991 -0.0436084420
## c4_F8R15 0.061667401 0.1873922112
## c4_F8R21 0.266561365 0.1206223149
## c4_F8R25 -0.040381631 -0.0710989119
## c4_F8R28 0.067240581 0.1725131991
## c4_F8R30 0.105936104 0.0422746403
## c4_F8R33 0.028529160 -0.0440149609
## c4_F8R37 0.210766211 0.0446878599
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL -0.26712156 -0.035849245
## 0_HF_PFOS -0.32929471 -0.051306536
## 0_LF_CTRL 0.17036143 -0.125448625
## 0_LF_PFOS 0.11043060 -0.014191644
## 12_HF_CTRL -0.02400607 0.027323800
## 12_HF_PFOS -0.12556017 0.004427384
## 12_LF_CTRL 0.18946867 0.062635559
## 12_LF_PFOS 0.11495994 0.136846318
## 16_HF_CTRL -0.16160738 -0.109848376
## 16_HF_PFOS -0.13288843 0.012375580
## 16_LF_CTRL 0.26562591 0.016818090
## 16_LF_PFOS 0.18334634 0.062216473
## 21_HF_CTRL -0.06584265 0.007635479
## 21_HF_PFOS -0.14366695 0.007812639
## 21_LF_CTRL 0.22269396 0.004218832
## 21_LF_PFOS 0.12924941 0.136267400
## 8_HF_CTRL -0.19329911 0.004265023
## 8_HF_PFOS -0.08477892 -0.016176409
## 8_LF_CTRL 0.15505748 0.069660277
## 8_LF_PFOS 0.09712955 0.128480849
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 19 0.17501 0.0092112 0.8314 0.667
## Residuals 148 1.63973 0.0110792## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 0.9807 0.05497 3.2516 0.002 **
## feed 1 4.3600 0.24440 57.8252 0.001 ***
## PFOS 1 0.1767 0.00991 2.3440 0.073 .
## day:feed 4 0.6243 0.03499 2.0698 0.018 *
## day:PFOS 3 0.1821 0.01021 0.8049 0.581
## feed:PFOS 1 0.1029 0.00577 1.3648 0.234
## day:feed:PFOS 3 0.1032 0.00578 0.4561 0.943
## Residual 150 11.3101 0.63397
## Total 167 17.8399 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Feces_no020 bray data..."
## $sites
## PCoA1 PCoA2
## c1_F12R09 -0.260243107 0.118325997
## c1_F12R19 -0.220346493 -0.215671422
## c1_F12R33 0.020720017 0.405436826
## c1_F12R42 0.474300067 -0.148186485
## c1_F16R08 -0.201270937 0.189985354
## c1_F16R20 -0.224646930 0.002407826
## c1_F16R21 -0.218918951 0.150719372
## c1_F16R22 -0.291686866 0.063217603
## c1_F16R33 -0.033762753 0.510973297
## c1_F16R36 0.425205246 0.083659732
## c1_F21R19 -0.290264794 -0.137834001
## c1_F21R23 -0.287942474 -0.083971493
## c1_F21R34 0.377780519 -0.007421493
## c1_F21R42 0.370054874 -0.087433425
## c1_F21R46 0.510971833 -0.179063342
## c1_F8R09 -0.298889297 -0.117288971
## c1_F8R12 -0.235676056 0.181835273
## c1_F8R17 -0.224915891 -0.011818540
## c1_F8R18 -0.318887884 -0.106308415
## c1_F8R22 -0.268309151 -0.045357068
## c1_F8R29 0.507914679 -0.098992847
## c1_F8R34 0.440106201 -0.126535629
## c1_F8R36 0.381718910 -0.056953983
## c1_F8R39 0.192446461 0.205657685
## c1_F8R40 0.386259142 -0.172747742
## c1_F8R46 0.454179317 -0.204821560
## c1_F8R48 0.380689601 -0.127306992
## c2_F12R07 -0.310116496 -0.092744607
## c2_F12R23 -0.203269031 -0.169505335
## c2_F12R31 0.464755901 -0.080199515
## c2_F12R45 0.289355730 0.077931905
## c2_F12R47 -0.008194561 0.374200616
## c2_F16R19 -0.267499235 -0.199550907
## c2_F16R42 0.379205363 -0.054679370
## c2_F16R45 0.105614218 0.251514607
## c2_F16R48 0.499738396 -0.128034737
## c2_F21R10 -0.197441280 0.026443826
## c2_F21R20 -0.257195439 -0.130773990
## c2_F21R21 -0.213601938 0.002110957
## c2_F21R24 -0.293727419 -0.220538359
## c2_F21R36 0.044967889 0.282618588
## c2_F8R02 -0.279525801 -0.042887440
## c2_F8R16 -0.248742320 -0.208053719
## c2_F8R20 -0.246439987 -0.036942936
## c2_F8R31 0.493797254 -0.137881246
## c2_F8R35 0.498504195 -0.178313596
## c2_F8R41 0.361291332 -0.093294668
## c2_F8R42 0.190537416 -0.019125767
## c2_F8R43 -0.128992877 0.061795292
## c2_F8R44 -0.150295487 0.084773465
## c2_F8R47 0.110847326 0.116455040
## c3_F12R08 -0.217951282 0.202576497
## c3_F12R10 -0.273085568 -0.063757010
## c3_F12R11 -0.264561156 -0.074112244
## c3_F12R20 -0.271949169 -0.253682327
## c3_F12R21 -0.246498236 -0.035513086
## c3_F12R22 -0.277834127 -0.026775403
## c3_F12R32 0.057021916 0.230621353
## c3_F16R07 -0.321913272 0.043872047
## c3_F16R11 -0.275627995 0.048828002
## c3_F16R12 -0.290571712 0.020257355
## c3_F16R23 -0.293504131 -0.196570745
## c3_F16R31 0.422401300 0.006995463
## c3_F16R32 0.379936011 0.019217951
## c3_F16R34 0.112107851 0.324459122
## c3_F16R47 0.099758462 0.338653702
## c3_F21R09 -0.245661775 0.078448508
## c3_F21R12 -0.253940766 -0.220161335
## c3_F21R22 -0.291822470 -0.113776597
## c3_F21R31 0.448737510 -0.049859463
## c3_F21R35 0.472718481 -0.133847102
## c3_F21R45 -0.163305223 0.329879516
## c3_F21R47 -0.114508574 0.190920730
## c3_F8R04 -0.201996580 0.009244254
## c3_F8R06 -0.193785903 -0.116666633
## c3_F8R07 -0.319046964 0.051946165
## c3_F8R10 -0.294650776 -0.024050284
## c3_F8R11 -0.279106707 -0.113506150
## c3_F8R13 -0.300897434 -0.096276287
## c3_F8R14 -0.268914955 -0.183828199
## c3_F8R19 -0.278632401 -0.163357490
## c3_F8R23 -0.269025566 -0.229271879
## c3_F8R24 -0.293892983 -0.080089967
## c3_F8R26 0.465858998 -0.085910373
## c3_F8R27 0.304561187 -0.083917526
## c3_F8R32 -0.007438834 0.081468998
## c3_F8R38 -0.094117225 0.318403358
## c3_F8R45 0.063933534 0.168369068
## c4_F12R12 -0.298160339 -0.111747382
## c4_F12R24 -0.261376342 -0.199747175
## c4_F12R34 0.342663210 0.088617308
## c4_F12R35 0.493051948 -0.040436189
## c4_F12R36 0.319475833 -0.007092181
## c4_F12R41 0.287818224 0.063888358
## c4_F12R46 0.390730188 -0.014274400
## c4_F12R48 0.490814733 -0.140601238
## c4_F16R09 -0.275282658 -0.069538730
## c4_F16R10 -0.263112620 0.033181729
## c4_F16R24 -0.273184554 -0.061724060
## c4_F16R35 0.533336368 -0.143061803
## c4_F16R41 0.358559034 -0.003315736
## c4_F16R46 0.449526647 -0.027116319
## c4_F21R07 -0.221600424 0.157934322
## c4_F21R08 -0.164658878 0.215565173
## c4_F21R11 -0.222255715 -0.117827061
## c4_F21R32 0.103177017 0.163239343
## c4_F21R33 0.004760655 0.390139402
## c4_F21R41 0.284859552 0.066654629
## c4_F21R48 0.454265104 -0.082300253
## c4_F8R01 -0.271896852 -0.247474661
## c4_F8R03 -0.271049552 -0.194630137
## c4_F8R05 -0.202230606 -0.036238631
## c4_F8R08 -0.243895767 0.073533280
## c4_F8R15 -0.273454352 -0.150224812
## c4_F8R21 -0.219402515 0.007780252
## c4_F8R25 0.271577453 0.145534647
## c4_F8R28 -0.103562314 0.081750609
## c4_F8R30 0.333526365 0.062760579
## c4_F8R33 0.145910715 0.270300903
## c4_F8R37 -0.101881459 0.237414583
##
## $centroids
## PCoA1 PCoA2
## 12_HF_CTRL 0.3418894 0.048869247
## 12_HF_PFOS 0.3502347 0.005855335
## 12_LF_CTRL -0.2781761 -0.030175982
## 12_LF_PFOS -0.2476581 -0.147527799
## 16_HF_CTRL 0.3605320 0.077497385
## 16_HF_PFOS 0.3510870 0.017519299
## 16_LF_CTRL -0.2806991 0.038700850
## 16_LF_PFOS -0.2639328 -0.040147664
## 21_HF_CTRL 0.2608792 0.089628692
## 21_HF_PFOS 0.2781565 0.007204765
## 21_LF_CTRL -0.2194902 0.036261955
## 21_LF_PFOS -0.2748977 -0.118396776
## 8_HF_CTRL 0.3574647 -0.035663638
## 8_HF_PFOS 0.1408762 0.051501046
## 8_LF_CTRL -0.2618648 -0.053024302
## 8_LF_PFOS -0.2708785 -0.112952823
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 15 0.09105 0.0060702 0.4415 0.9626
## Residuals 104 1.42976 0.0137477## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## feed 1 8.6249 0.30107 51.7273 0.001 ***
## PFOS 1 0.4114 0.01436 2.4675 0.027 *
## feed:PFOS 1 0.2694 0.00940 1.6155 0.115
## Residual 116 19.3417 0.67516
## Total 119 28.6474 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Feces_no020 jac data..."
## $sites
## PCoA1 PCoA2
## c1_F12R09 -0.0224380735 -0.310952280
## c1_F12R19 0.0002682101 -0.336598863
## c1_F12R33 -0.1614632317 -0.219392275
## c1_F12R42 -0.3372989725 -0.116576186
## c1_F16R08 0.0259979284 -0.309597676
## c1_F16R20 -0.0504460304 -0.302331132
## c1_F16R21 -0.0357424639 -0.310078769
## c1_F16R22 0.0359322280 -0.319701853
## c1_F16R33 -0.1505992905 -0.211466111
## c1_F16R36 -0.2151184062 -0.196336050
## c1_F21R19 -0.0100997846 -0.326301613
## c1_F21R23 -0.0135530896 -0.314773218
## c1_F21R34 -0.1815296953 -0.233236104
## c1_F21R42 -0.2358389315 -0.206152172
## c1_F21R46 -0.3683027139 -0.102795600
## c1_F8R09 -0.0177219726 -0.321018140
## c1_F8R12 -0.0594664932 -0.285008491
## c1_F8R17 -0.0596461608 -0.290613528
## c1_F8R18 -0.0044150055 -0.296879119
## c1_F8R22 -0.0883705276 -0.259543203
## c1_F8R29 -0.3104509145 -0.139311163
## c1_F8R34 -0.3071234370 -0.158036836
## c1_F8R36 -0.2933898274 -0.151000129
## c1_F8R39 -0.1580035280 -0.227056198
## c1_F8R40 -0.1275247138 -0.243398721
## c1_F8R46 -0.3673954792 -0.120683862
## c1_F8R48 -0.2623435048 -0.173426510
## c2_F12R07 0.1183108161 -0.057506781
## c2_F12R23 0.0933168894 -0.058053916
## c2_F12R31 -0.2591328774 0.114949764
## c2_F12R45 -0.0704565333 0.055568473
## c2_F12R47 -0.0045312386 0.018262173
## c2_F16R19 0.1588895481 -0.094301919
## c2_F16R42 -0.1161442161 0.064129002
## c2_F16R45 -0.0124486705 0.027301295
## c2_F16R48 -0.2754035466 0.143330966
## c2_F21R10 0.1240461559 -0.055981602
## c2_F21R20 0.1471991626 -0.058062752
## c2_F21R21 0.1568390931 -0.056986674
## c2_F21R24 0.1572120658 -0.077828942
## c2_F21R36 -0.0523518938 0.037957393
## c2_F8R02 0.1389196962 -0.036917312
## c2_F8R16 0.1101713674 -0.064719476
## c2_F8R20 0.1112303760 -0.072392614
## c2_F8R31 -0.2187204513 0.120028445
## c2_F8R35 -0.3082591989 0.136050289
## c2_F8R41 -0.1796897556 0.054152182
## c2_F8R42 -0.2078516297 0.129917151
## c2_F8R43 0.0321264857 -0.017727210
## c2_F8R44 0.0488437713 -0.001924463
## c2_F8R47 -0.0052345650 0.032204604
## c3_F12R08 0.2123241920 0.049362971
## c3_F12R10 0.2426295244 0.063963850
## c3_F12R11 0.2420495268 0.032615121
## c3_F12R20 0.2071794119 0.039319312
## c3_F12R21 0.2269175709 0.031790371
## c3_F12R22 0.2503024278 0.046263491
## c3_F12R32 0.0219543567 0.155491334
## c3_F16R07 0.2443580218 0.034181858
## c3_F16R11 0.2533123662 0.034643772
## c3_F16R12 0.2128855865 0.031097539
## c3_F16R23 0.2463641331 0.038181599
## c3_F16R31 -0.1719465613 0.215192392
## c3_F16R32 -0.0495137815 0.161198726
## c3_F16R34 -0.0645075824 0.185178410
## c3_F16R47 0.0750040985 0.131871448
## c3_F21R09 0.2207706358 0.041550462
## c3_F21R12 0.2203538692 0.028691635
## c3_F21R22 0.2628854917 0.045231897
## c3_F21R31 -0.1728944446 0.229588936
## c3_F21R35 -0.1684636492 0.203417278
## c3_F21R45 0.1363355425 0.109023623
## c3_F21R47 0.1301692145 0.069914866
## c3_F8R04 0.1657012085 0.072666240
## c3_F8R06 0.2422753594 -0.002676290
## c3_F8R07 0.1933426629 0.042264600
## c3_F8R10 0.1953005259 0.075258721
## c3_F8R11 0.2521113537 0.034996362
## c3_F8R13 0.2104638645 0.040358199
## c3_F8R14 0.2179551053 0.020917841
## c3_F8R19 0.2254882063 0.045296974
## c3_F8R23 0.1750161795 0.054777405
## c3_F8R24 0.2146418544 0.047117001
## c3_F8R26 -0.1572697624 0.198276247
## c3_F8R27 -0.1140568694 0.206400275
## c3_F8R32 0.0184568385 0.158677544
## c3_F8R38 0.0795912440 0.133883373
## c3_F8R45 0.0676704280 0.132252720
## c4_F12R12 0.1389251895 0.018344255
## c4_F12R24 0.1636995942 -0.031439088
## c4_F12R34 -0.2139302896 0.186884995
## c4_F12R35 -0.2819223560 0.196689473
## c4_F12R36 -0.1929715559 0.164175559
## c4_F12R41 -0.0674047607 0.104884492
## c4_F12R46 -0.2566336364 0.187870086
## c4_F12R48 -0.2621495130 0.215443202
## c4_F16R09 0.1590506241 0.009463891
## c4_F16R10 0.1855144877 0.023135007
## c4_F16R24 0.1906216839 0.028801340
## c4_F16R35 -0.2681079758 0.220950668
## c4_F16R41 -0.0947546882 0.120653328
## c4_F16R46 -0.2532103171 0.196441676
## c4_F21R07 0.1685727902 0.011298656
## c4_F21R08 0.1651659643 0.002047485
## c4_F21R11 0.1953055474 -0.016317902
## c4_F21R32 -0.0861834878 0.129080325
## c4_F21R33 -0.0701564399 0.116430204
## c4_F21R41 -0.1209955352 0.119595017
## c4_F21R48 -0.2745184847 0.211980274
## c4_F8R01 0.0993523032 0.005933771
## c4_F8R03 0.1103621882 0.026721411
## c4_F8R05 0.1248631343 0.055610921
## c4_F8R08 0.1320957667 0.032692549
## c4_F8R15 0.1364972623 0.040086480
## c4_F8R21 0.1180763760 0.044585836
## c4_F8R25 -0.0247193687 0.116403559
## c4_F8R28 -0.0222057243 0.059118929
## c4_F8R30 -0.2206882304 0.165447396
## c4_F8R33 -0.0665901467 0.107195585
## c4_F8R37 0.0130844786 0.092370242
##
## $centroids
## PCoA1 PCoA2
## 12_HF_CTRL -0.19314146 0.122365301
## 12_HF_PFOS -0.16496572 0.086692512
## 12_LF_CTRL 0.16824840 -0.018256932
## 12_LF_PFOS 0.16773573 -0.035471393
## 16_HF_CTRL -0.14783390 0.075956149
## 16_HF_PFOS -0.11233098 0.109779735
## 16_LF_CTRL 0.19106100 -0.014139192
## 16_LF_PFOS 0.08373404 -0.171660316
## 21_HF_CTRL -0.11819722 0.086077938
## 21_HF_PFOS -0.12052767 0.032818888
## 21_LF_CTRL 0.18026228 0.001166181
## 21_LF_PFOS 0.12029965 -0.124454536
## 8_HF_CTRL -0.17310501 0.066183602
## 8_HF_PFOS -0.08192784 -0.013483440
## 8_LF_CTRL 0.13940561 -0.013869444
## 8_LF_PFOS 0.12614689 -0.044061242
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 15 0.071986 0.0047991 1.8429 0.03807 *
## Residuals 104 0.270824 0.0026041
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## feed 1 2.9384 0.13751 19.1477 0.001 ***
## PFOS 1 0.3217 0.01505 2.0962 0.008 **
## feed:PFOS 1 0.3073 0.01438 2.0027 0.023 *
## Residual 116 17.8016 0.83305
## Total 119 21.3690 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Feces_no020 unif data..."
## $sites
## PCoA1 PCoA2
## c1_F12R09 0.004771211 -0.146784505
## c1_F12R19 0.045988673 -0.165475109
## c1_F12R33 -0.054181786 -0.125360979
## c1_F12R42 -0.236660194 -0.076194658
## c1_F16R08 0.049799297 -0.184037084
## c1_F16R20 -0.012510830 -0.145062217
## c1_F16R21 0.010416634 -0.165045831
## c1_F16R22 0.060912124 -0.185549859
## c1_F16R33 -0.047884285 -0.114580381
## c1_F16R36 -0.093566280 -0.135635170
## c1_F21R19 0.025300467 -0.176645229
## c1_F21R23 0.052597867 -0.168557847
## c1_F21R34 -0.058527625 -0.133035503
## c1_F21R42 -0.113816969 -0.128410465
## c1_F21R46 -0.256630301 -0.082072417
## c1_F8R09 0.034681352 -0.151082655
## c1_F8R12 0.012934006 -0.178011369
## c1_F8R17 -0.051481684 -0.151715101
## c1_F8R18 0.031424234 -0.190779243
## c1_F8R22 -0.070574308 -0.115792607
## c1_F8R29 -0.160018587 -0.103307138
## c1_F8R34 -0.178357060 -0.117197001
## c1_F8R36 -0.194563704 -0.091550813
## c1_F8R39 -0.053496623 -0.115407810
## c1_F8R40 -0.087757897 -0.141268108
## c1_F8R46 -0.255976491 -0.055540343
## c1_F8R48 -0.173116435 -0.117156533
## c2_F12R07 0.060445274 0.004314094
## c2_F12R23 0.091646709 0.003863705
## c2_F12R31 -0.199658133 0.063261616
## c2_F12R45 -0.020712856 0.028989756
## c2_F12R47 0.006263683 0.006376647
## c2_F16R19 0.138360233 -0.008752775
## c2_F16R42 -0.047385251 0.033794212
## c2_F16R45 0.032270488 0.023359545
## c2_F16R48 -0.210269983 0.031855041
## c2_F21R10 0.095199012 -0.012651398
## c2_F21R20 0.147688071 0.017788160
## c2_F21R21 0.133045928 0.001798670
## c2_F21R24 0.129769793 -0.014882398
## c2_F21R36 -0.009772215 0.024072480
## c2_F8R02 0.103899113 0.011993256
## c2_F8R16 0.114283891 0.012089015
## c2_F8R20 0.088839782 -0.017553471
## c2_F8R31 -0.210353373 0.040337121
## c2_F8R35 -0.233674483 0.031484748
## c2_F8R41 -0.063182421 0.026627626
## c2_F8R42 -0.163213079 0.097046799
## c2_F8R43 0.063459916 0.011628316
## c2_F8R44 0.038119215 0.040007857
## c2_F8R47 0.018114339 0.038256632
## c3_F12R08 0.085638011 0.012759089
## c3_F12R10 0.132570907 0.013248973
## c3_F12R11 0.134944721 0.009651234
## c3_F12R20 0.095718289 -0.014711038
## c3_F12R21 0.147726849 -0.022047825
## c3_F12R22 0.113711396 -0.004279368
## c3_F12R32 -0.022265948 0.062734583
## c3_F16R07 0.131430876 0.016227290
## c3_F16R11 0.138569315 -0.024187724
## c3_F16R12 0.128013449 -0.031372148
## c3_F16R23 0.130992759 0.013543026
## c3_F16R31 -0.225305667 0.051562274
## c3_F16R32 -0.063865415 -0.002251586
## c3_F16R34 -0.095018411 0.071524851
## c3_F16R47 0.013859687 0.017038879
## c3_F21R09 0.121394614 0.028155255
## c3_F21R12 0.094073348 -0.015198477
## c3_F21R22 0.148770430 -0.006791916
## c3_F21R31 -0.211012083 0.048335425
## c3_F21R35 -0.199293291 0.100526703
## c3_F21R45 0.057962587 0.010753842
## c3_F21R47 0.039127966 -0.043778642
## c3_F8R04 0.057275515 0.025876464
## c3_F8R06 0.104973426 -0.031495347
## c3_F8R07 0.056357273 0.024128416
## c3_F8R10 0.087757894 -0.003452867
## c3_F8R11 0.136764099 0.004829008
## c3_F8R13 0.083993752 0.005649259
## c3_F8R14 0.096969568 -0.002728426
## c3_F8R19 0.107570727 0.013649818
## c3_F8R23 0.056423088 -0.014849872
## c3_F8R24 0.072670559 0.004542042
## c3_F8R26 -0.179851292 0.040537250
## c3_F8R27 -0.154385938 0.048122023
## c3_F8R32 -0.050712425 0.063119332
## c3_F8R38 0.024782995 0.057531561
## c3_F8R45 0.002587751 0.043969113
## c4_F12R12 0.157989885 0.057411856
## c4_F12R24 0.147940891 0.047892133
## c4_F12R34 -0.138329526 0.138903626
## c4_F12R35 -0.221651168 0.056969826
## c4_F12R36 -0.116360962 0.088453113
## c4_F12R41 -0.040058072 0.076841215
## c4_F12R46 -0.169113545 0.088780942
## c4_F12R48 -0.179426332 0.115199084
## c4_F16R09 0.139621141 0.062632668
## c4_F16R10 0.137577504 0.072728233
## c4_F16R24 0.185012245 0.074022386
## c4_F16R35 -0.211720506 0.102855660
## c4_F16R41 -0.027445703 0.057802148
## c4_F16R46 -0.203281314 0.120134137
## c4_F21R07 0.149693402 0.051333571
## c4_F21R08 0.109797448 0.046270114
## c4_F21R11 0.193518809 0.050841494
## c4_F21R32 -0.061918245 0.113348287
## c4_F21R33 -0.002476214 0.088619950
## c4_F21R41 -0.019501538 0.072033125
## c4_F21R48 -0.181547944 0.138019408
## c4_F8R01 0.093188201 0.057260288
## c4_F8R03 0.082153782 0.066326537
## c4_F8R05 0.107513879 0.100042454
## c4_F8R08 0.063790732 0.069855996
## c4_F8R15 0.162269314 0.107464165
## c4_F8R21 0.151260246 0.094412177
## c4_F8R25 0.022128499 0.088697328
## c4_F8R28 0.023607646 0.038818912
## c4_F8R30 -0.136019316 0.067199991
## c4_F8R33 0.006299314 0.068717018
## c4_F8R37 0.041677602 0.115392404
##
## $centroids
## PCoA1 PCoA2
## 12_HF_CTRL -0.13510997 0.058543773
## 12_HF_PFOS -0.11255400 0.045764882
## 12_LF_CTRL 0.10168405 -0.001874690
## 12_LF_PFOS 0.10953004 -0.019743159
## 16_HF_CTRL -0.11954153 -0.003351575
## 16_HF_PFOS -0.06178767 0.044801106
## 16_LF_CTRL 0.12470729 -0.010360385
## 16_LF_PFOS 0.09105707 -0.062655986
## 21_HF_CTRL -0.08194233 0.041334611
## 21_HF_PFOS -0.07272083 -0.010528526
## 21_LF_CTRL 0.13086793 0.029542740
## 21_LF_PFOS 0.11293446 -0.045515395
## 8_HF_CTRL -0.12994374 0.011324441
## 8_HF_PFOS -0.04318605 0.004184494
## 8_LF_CTRL 0.08248580 0.004796034
## 8_LF_PFOS 0.07426542 -0.016007346
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 15 0.04501 0.0030006 1.8266 0.04028 *
## Residuals 104 0.17084 0.0016427
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## feed 1 1.2921 0.17998 26.2310 0.001 ***
## PFOS 1 0.0694 0.00966 1.4084 0.156
## feed:PFOS 1 0.1037 0.01444 2.1045 0.023 *
## Residual 116 5.7138 0.79592
## Total 119 7.1789 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Feces_no020 wuf data..."
## $sites
## PCoA1 PCoA2
## c1_F12R09 0.285314373 -0.177010389
## c1_F12R19 -0.237280621 0.014656649
## c1_F12R33 0.267107714 -0.404709034
## c1_F12R42 -0.469463565 -0.095996795
## c1_F16R08 0.277833371 -0.127223533
## c1_F16R20 0.134807826 0.033953586
## c1_F16R21 0.271833661 -0.203553166
## c1_F16R22 0.164136106 -0.056626434
## c1_F16R33 0.297034140 -0.455969960
## c1_F16R36 -0.241199810 -0.233620813
## c1_F21R19 -0.121124477 0.042379569
## c1_F21R23 0.136642046 -0.014797553
## c1_F21R34 -0.235507529 -0.036329561
## c1_F21R42 -0.330168585 -0.069113814
## c1_F21R46 -0.496736812 -0.087900552
## c1_F8R09 -0.064372508 0.057769998
## c1_F8R12 0.257585147 -0.253876290
## c1_F8R17 0.258777567 -0.081997782
## c1_F8R18 -0.067191563 0.040305882
## c1_F8R22 -0.139667736 -0.066575280
## c1_F8R29 -0.416314514 -0.121706719
## c1_F8R34 -0.398437318 -0.099366651
## c1_F8R36 -0.273997958 -0.047689644
## c1_F8R39 -0.058982758 -0.239093165
## c1_F8R40 -0.408234894 -0.095578600
## c1_F8R46 -0.431478905 -0.068979694
## c1_F8R48 -0.289286502 -0.092597434
## c2_F12R07 0.087009948 0.026272006
## c2_F12R23 0.116260853 0.104924938
## c2_F12R31 -0.220108626 0.026418294
## c2_F12R45 -0.136425617 -0.064770539
## c2_F12R47 0.277658378 -0.289645848
## c2_F16R19 -0.114702567 0.156314795
## c2_F16R42 -0.184820964 0.051817457
## c2_F16R45 -0.001650121 -0.125334339
## c2_F16R48 -0.359041938 -0.029079220
## c2_F21R10 0.103608780 -0.018415437
## c2_F21R20 0.169762229 0.105298587
## c2_F21R21 0.199170665 0.128664840
## c2_F21R24 0.011770445 0.155859597
## c2_F21R36 0.076055079 -0.038797161
## c2_F8R02 0.136655310 0.079151798
## c2_F8R16 -0.146248819 0.128468069
## c2_F8R20 0.183777658 0.024335472
## c2_F8R31 -0.474236175 -0.075462768
## c2_F8R35 -0.499310725 -0.068167375
## c2_F8R41 -0.306608136 0.063072084
## c2_F8R42 0.038690255 0.125024521
## c2_F8R43 -0.161000361 -0.033763195
## c2_F8R44 -0.114955430 -0.022929644
## c2_F8R47 -0.080880382 -0.067252854
## c3_F12R08 0.291581193 -0.139970062
## c3_F12R10 0.100395295 0.139665136
## c3_F12R11 0.139737908 0.103975944
## c3_F12R20 -0.186219024 0.115367392
## c3_F12R21 0.252471365 0.140934476
## c3_F12R22 0.231782405 0.124324251
## c3_F12R32 0.030800362 -0.014006544
## c3_F16R07 0.238276872 -0.044051902
## c3_F16R11 0.237252131 -0.054296097
## c3_F16R12 0.334374424 -0.042454600
## c3_F16R23 0.164652197 0.158912536
## c3_F16R31 -0.224406385 -0.103908997
## c3_F16R32 -0.329565889 -0.044032443
## c3_F16R34 0.178295038 -0.086395823
## c3_F16R47 0.133328820 -0.253400406
## c3_F21R09 0.234188907 -0.011468896
## c3_F21R12 -0.023415068 0.087411364
## c3_F21R22 0.144095233 0.179458087
## c3_F21R31 -0.257770129 -0.015574791
## c3_F21R35 -0.254326932 0.071474624
## c3_F21R45 0.196965562 -0.108753126
## c3_F21R47 0.142566531 -0.007043546
## c3_F8R04 0.252853637 0.106520422
## c3_F8R06 0.035639963 0.054449422
## c3_F8R07 0.338087601 -0.003458032
## c3_F8R10 0.217857089 0.036600947
## c3_F8R11 0.162095743 0.103941598
## c3_F8R13 0.103580485 0.148443381
## c3_F8R14 0.017525327 0.152280829
## c3_F8R19 0.150144700 0.166936343
## c3_F8R23 0.131163878 0.214541600
## c3_F8R24 0.041646600 0.088872717
## c3_F8R26 -0.304307481 -0.009175018
## c3_F8R27 -0.127095876 0.136361349
## c3_F8R32 -0.043151926 0.075165372
## c3_F8R38 0.236425643 -0.047210141
## c3_F8R45 0.044153552 0.043604164
## c4_F12R12 0.179970014 0.080132597
## c4_F12R24 0.109009773 0.126668061
## c4_F12R34 -0.032648324 0.020910710
## c4_F12R35 -0.158576972 0.031321425
## c4_F12R36 -0.022235394 0.087058366
## c4_F12R41 -0.081291000 0.162650967
## c4_F12R46 -0.060049749 0.078769675
## c4_F12R48 -0.369480196 -0.032540481
## c4_F16R09 0.123847941 0.108171915
## c4_F16R10 0.253769378 0.056354020
## c4_F16R24 0.266811683 0.070229488
## c4_F16R35 -0.398466856 -0.041671438
## c4_F16R41 -0.269356025 0.033869411
## c4_F16R46 -0.116052144 0.077508184
## c4_F21R07 0.273587320 -0.144235527
## c4_F21R08 0.332121926 -0.207398265
## c4_F21R11 0.238547179 0.164435180
## c4_F21R32 -0.023502204 0.006760100
## c4_F21R33 0.256243727 -0.158630370
## c4_F21R41 -0.239964829 0.021389583
## c4_F21R48 -0.142934149 0.080573805
## c4_F8R01 -0.203907030 0.107922134
## c4_F8R03 0.049872701 0.115678125
## c4_F8R05 0.234539471 0.058188589
## c4_F8R08 0.015425348 -0.065438771
## c4_F8R15 0.031898097 0.172711717
## c4_F8R21 0.238532540 0.084840092
## c4_F8R25 -0.072951638 -0.102950627
## c4_F8R28 0.040055700 0.154802777
## c4_F8R30 0.070139485 0.024595016
## c4_F8R33 -0.008457974 -0.063289799
## c4_F8R37 0.181766816 0.025814913
##
## $centroids
## PCoA1 PCoA2
## 12_HF_CTRL -0.05855005 0.010456780
## 12_HF_PFOS -0.15499043 -0.012597819
## 12_LF_CTRL 0.16331794 0.036664226
## 12_LF_PFOS 0.09062577 0.112613568
## 16_HF_CTRL -0.19549471 -0.132213441
## 16_HF_PFOS -0.16296261 -0.008807005
## 16_LF_CTRL 0.24332850 -0.016143497
## 16_LF_PFOS 0.15675645 0.036646444
## 21_HF_CTRL -0.09928002 -0.017080690
## 21_HF_PFOS -0.17270803 -0.017461641
## 21_LF_CTRL 0.19708813 -0.022629010
## 21_LF_PFOS 0.10449075 0.110026608
## 8_HF_CTRL -0.22192806 -0.017827049
## 8_HF_PFOS -0.11673465 -0.034757587
## 8_LF_CTRL 0.12838776 0.045014259
## 8_LF_PFOS 0.07082969 0.109047769
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 15 0.12532 0.0083548 0.7142 0.7652
## Residuals 104 1.21656 0.0116977## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## feed 1 2.7287 0.22634 34.9852 0.001 ***
## PFOS 1 0.1767 0.01466 2.2660 0.052 .
## feed:PFOS 1 0.1029 0.00854 1.3194 0.255
## Residual 116 9.0475 0.75047
## Total 119 12.0559 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 0.170779574 -0.160792525
## c1_F0R30 -0.255679839 -0.064461901
## c1_F0R33 0.161473072 -0.012677126
## c1_F0R35 -0.249482919 -0.216916250
## c1_F0R36 -0.325827487 -0.108555065
## c1_F0R38 -0.151968584 -0.215110941
## c1_F0R40 0.099270253 -0.129954558
## c1_F0R42 -0.338139168 -0.149669132
## c1_F0R44 -0.058115625 0.009293722
## c1_F0R45 -0.319925020 -0.146077536
## c1_F0R47 -0.244450167 -0.197503217
## c1_F12R33 0.399973992 -0.011503021
## c1_F12R42 -0.289731541 -0.143757471
## c1_F16R33 0.431677016 0.010075672
## c1_F16R36 -0.063170928 -0.079468614
## c1_F21R34 -0.069445356 -0.026303817
## c1_F21R42 -0.116596504 -0.091986066
## c1_F21R46 -0.333242070 -0.121798038
## c1_F8R29 -0.281410231 -0.074745799
## c1_F8R34 -0.214053196 -0.083312554
## c1_F8R36 -0.119202980 -0.034534015
## c1_F8R39 0.208935491 -0.019312967
## c1_F8R40 -0.197746463 -0.174327274
## c1_F8R46 -0.296208039 -0.095668720
## c1_F8R48 -0.147502206 -0.016364413
## c2_F0R25 -0.096545295 -0.105111761
## c2_F0R29 -0.275443628 0.090153547
## c2_F0R34 -0.240394590 -0.022450492
## c2_F0R37 0.072005616 -0.083605143
## c2_F0R39 -0.025284180 -0.036981995
## c2_F0R43 -0.159500627 -0.200382900
## c2_F0R48 -0.041326853 0.193746042
## c2_F12R31 -0.205109907 0.146435307
## c2_F12R45 0.082112906 -0.018319066
## c2_F12R47 0.461953153 0.014801641
## c2_F16R42 -0.100588447 0.109857320
## c2_F16R45 0.349574402 -0.023572676
## c2_F16R48 -0.287680607 0.041370272
## c2_F21R36 0.390342807 0.032668410
## c2_F8R31 -0.309123010 -0.111463959
## c2_F8R35 -0.327794603 -0.109998211
## c2_F8R41 -0.095749396 -0.078504734
## c2_F8R42 0.111827117 0.354526590
## c2_F8R43 0.429856354 -0.187040804
## c2_F8R44 0.448720480 -0.190891228
## c2_F8R47 0.268333961 -0.044031425
## c3_F0R26 -0.134331277 0.127670145
## c3_F0R41 -0.337110378 -0.093977462
## c3_F12R32 0.382612796 -0.032048211
## c3_F16R31 -0.121421151 0.097328701
## c3_F16R32 -0.035571530 -0.096298976
## c3_F16R34 0.291256391 0.260945991
## c3_F16R47 0.327934575 0.072023444
## c3_F21R31 -0.181974198 0.106632757
## c3_F21R35 -0.237642923 0.188140190
## c3_F21R45 0.518597416 -0.086287235
## c3_F21R47 0.460214233 -0.084460861
## c3_F8R26 -0.211828036 0.054605026
## c3_F8R27 -0.019814785 0.251520096
## c3_F8R32 0.329319958 -0.043241145
## c3_F8R38 0.510915084 -0.050471605
## c3_F8R45 0.315759763 0.016495660
## c4_F0R27 -0.165550698 0.153379803
## c4_F0R31 -0.177625564 0.049812049
## c4_F0R32 -0.170995791 -0.124817307
## c4_F0R46 -0.333874617 0.024569088
## c4_F12R34 0.029442812 0.279684793
## c4_F12R35 -0.180509243 0.256697380
## c4_F12R36 0.004598127 0.315030675
## c4_F12R41 0.079847981 -0.060496939
## c4_F12R46 -0.055496004 0.336534498
## c4_F12R48 -0.284814077 0.018528079
## c4_F16R35 -0.327478882 0.042290880
## c4_F16R41 -0.035321692 -0.139060775
## c4_F16R46 -0.120645017 0.313648895
## c4_F21R32 0.314095659 -0.023511319
## c4_F21R33 0.441170798 0.169902073
## c4_F21R41 0.068933134 -0.078898401
## c4_F21R48 -0.172001681 0.280341905
## c4_F8R25 0.124185448 0.012512240
## c4_F8R28 0.430665673 -0.189601830
## c4_F8R30 0.015972194 0.367250250
## c4_F8R33 0.321401495 -0.003418344
## c4_F8R37 0.486687286 -0.104727314
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL -0.182897039 -0.02918772
## 0_HF_PFOS -0.180539915 -0.10431261
## 12_HF_CTRL -0.001787459 0.20982117
## 12_HF_PFOS -0.040432243 0.02408864
## 16_HF_CTRL -0.038084865 0.03326614
## 16_HF_PFOS -0.035878968 0.07091060
## 21_HF_CTRL 0.076492656 0.07124894
## 21_HF_PFOS 0.008410705 -0.03449716
## 8_HF_CTRL -0.088024306 -0.00654190
## 8_HF_PFOS 0.170877687 -0.05364933
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 9 0.23708 0.026343 1.4613 0.1785
## Residuals 74 1.33403 0.018027## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 1.6543 0.11877 2.6837 0.002 **
## PFOS 1 0.2660 0.01910 1.7258 0.135
## day:PFOS 3 0.4501 0.03231 0.9736 0.449
## Residual 75 11.5582 0.82982
## Total 83 13.9286 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 -0.106285445 -0.305585683
## c1_F0R30 -0.314871928 -0.046719856
## c1_F0R33 -0.160693419 -0.240720149
## c1_F0R35 -0.131373712 -0.279195185
## c1_F0R36 -0.305794642 0.008515215
## c1_F0R38 -0.175255181 -0.216974642
## c1_F0R40 -0.093699725 -0.289082991
## c1_F0R42 -0.298587469 -0.038867581
## c1_F0R44 -0.286274634 -0.062412127
## c1_F0R45 -0.301614705 -0.031794883
## c1_F0R47 -0.126149553 -0.230625221
## c1_F12R33 -0.101192020 -0.249315352
## c1_F12R42 -0.270939619 -0.061433952
## c1_F16R33 -0.098098183 -0.234743641
## c1_F16R36 -0.170192588 -0.173540647
## c1_F21R34 -0.145471576 -0.206067830
## c1_F21R42 -0.146605080 -0.204560297
## c1_F21R46 -0.289978977 -0.035073191
## c1_F8R29 -0.272352109 -0.032126829
## c1_F8R34 -0.231369630 -0.100429696
## c1_F8R36 -0.242953293 -0.069426589
## c1_F8R39 -0.115854476 -0.267376075
## c1_F8R40 -0.149346630 -0.241465216
## c1_F8R46 -0.301948964 0.002523010
## c1_F8R48 -0.252113541 -0.092977606
## c2_F0R25 0.172698949 -0.132116596
## c2_F0R29 -0.045214909 0.163125227
## c2_F0R34 -0.002241232 0.100265308
## c2_F0R37 0.161492635 -0.150898542
## c2_F0R39 0.121022806 -0.056652308
## c2_F0R43 0.166011491 -0.133746636
## c2_F0R48 0.011471022 0.113303494
## c2_F12R31 -0.060876961 0.159839803
## c2_F12R45 0.197227443 -0.122996703
## c2_F12R47 0.225669579 -0.130542799
## c2_F16R42 0.087668708 0.002944756
## c2_F16R45 0.214368898 -0.133771010
## c2_F16R48 -0.087110440 0.181102569
## c2_F21R36 0.210211918 -0.117710965
## c2_F8R31 -0.069467731 0.163555928
## c2_F8R35 -0.115312365 0.221436322
## c2_F8R41 0.048782595 0.005789185
## c2_F8R42 0.022490309 0.126438857
## c2_F8R43 0.211102495 -0.222417728
## c2_F8R44 0.223408165 -0.203171858
## c2_F8R47 0.179656978 -0.120549482
## c3_F0R26 -0.048197084 0.219519702
## c3_F0R41 -0.097597439 0.220204025
## c3_F12R32 0.183907805 -0.014249816
## c3_F16R31 -0.029803363 0.194870242
## c3_F16R32 0.126423012 0.020003090
## c3_F16R34 0.097330124 0.092178626
## c3_F16R47 0.222746957 -0.049893218
## c3_F21R31 -0.033069911 0.219429656
## c3_F21R35 -0.026078878 0.225657272
## c3_F21R45 0.240161523 -0.059844755
## c3_F21R47 0.220827939 -0.099802970
## c3_F8R26 -0.041129964 0.226481541
## c3_F8R27 0.028207541 0.196668014
## c3_F8R32 0.172053410 0.055832775
## c3_F8R38 0.213966497 -0.043341392
## c3_F8R45 0.177448830 -0.010140292
## c4_F0R27 0.034868367 0.168350127
## c4_F0R31 0.021847798 0.183482184
## c4_F0R32 0.115463913 0.067291895
## c4_F0R46 -0.141200970 0.241075134
## c4_F12R34 0.052742279 0.179397593
## c4_F12R35 -0.047908865 0.251384500
## c4_F12R36 0.083054581 0.154199688
## c4_F12R41 0.202115915 0.003197498
## c4_F12R46 -0.018329513 0.252743962
## c4_F12R48 -0.078896829 0.253137288
## c4_F16R35 -0.083924196 0.248158411
## c4_F16R41 0.186105814 0.018740497
## c4_F16R46 -0.048339820 0.244285375
## c4_F21R32 0.177119715 0.034758326
## c4_F21R33 0.216512799 0.029505938
## c4_F21R41 0.216285406 -0.003788999
## c4_F21R48 -0.029743169 0.257838016
## c4_F8R25 0.215875787 -0.022820350
## c4_F8R28 0.222201363 -0.066785383
## c4_F8R30 0.022260462 0.212293629
## c4_F8R33 0.227167858 -0.040603438
## c4_F8R37 0.263481052 -0.073164200
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL -0.063005968 -0.001156489
## 0_HF_PFOS -0.099993531 -0.059764306
## 12_HF_CTRL 0.018419809 0.106533615
## 12_HF_PFOS 0.046464326 0.039654234
## 16_HF_CTRL -0.021382582 0.028826483
## 16_HF_PFOS 0.097069905 0.039172511
## 21_HF_CTRL 0.077468762 0.028814302
## 21_HF_PFOS 0.042419814 -0.023470420
## 8_HF_CTRL -0.009254061 0.064130468
## 8_HF_PFOS 0.053294870 -0.099305643
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 9 0.008052 0.00089471 0.5252 0.8518
## Residuals 74 0.126069 0.00170363## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 1.1302 0.07739 1.6618 0.006 **
## PFOS 1 0.3148 0.02156 1.8517 0.028 *
## day:PFOS 3 0.4058 0.02779 0.7956 0.861
## Residual 75 12.7524 0.87325
## Total 83 14.6033 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 0.08120687 -0.179082261
## c1_F0R30 -0.12600132 -0.168521488
## c1_F0R33 0.03119817 -0.175307432
## c1_F0R35 0.06214721 -0.162124507
## c1_F0R36 -0.18044185 -0.100150691
## c1_F0R38 -0.01182346 -0.175237762
## c1_F0R40 0.07987445 -0.155828295
## c1_F0R42 -0.12575382 -0.131873826
## c1_F0R44 -0.11004175 -0.135445289
## c1_F0R45 -0.14559457 -0.136907093
## c1_F0R47 0.04123319 -0.187157330
## c1_F12R33 0.11220528 -0.145670003
## c1_F12R42 -0.09155129 -0.105414292
## c1_F16R33 0.08743938 -0.121213622
## c1_F16R36 0.02442756 -0.132064236
## c1_F21R34 0.05365881 -0.114749703
## c1_F21R42 0.06254568 -0.135321870
## c1_F21R46 -0.11260821 -0.120094761
## c1_F8R29 -0.06471617 -0.113681024
## c1_F8R34 -0.08284766 -0.119906148
## c1_F8R36 -0.07986454 -0.112512405
## c1_F8R39 0.06866140 -0.111861743
## c1_F8R40 -0.02181616 -0.146604452
## c1_F8R46 -0.15546844 -0.068452966
## c1_F8R48 -0.11090667 -0.109182741
## c2_F0R25 0.10875704 -0.011544146
## c2_F0R29 -0.12139812 0.067491178
## c2_F0R34 -0.03326770 0.013930344
## c2_F0R37 0.14564753 0.010153467
## c2_F0R39 0.04149819 0.007277493
## c2_F0R43 0.16137143 -0.054622312
## c2_F0R48 -0.09310900 0.057289699
## c2_F12R31 -0.10998816 0.055256011
## c2_F12R45 0.13297215 0.008609684
## c2_F12R47 0.17236432 0.037809992
## c2_F16R42 0.05299340 0.044719606
## c2_F16R45 0.17022601 0.022274057
## c2_F16R48 -0.12677287 0.044876170
## c2_F21R36 0.16217743 0.050716314
## c2_F8R31 -0.14287202 0.026139018
## c2_F8R35 -0.19466824 0.048217916
## c2_F8R41 0.02844496 0.030836557
## c2_F8R42 -0.03164916 0.066521240
## c2_F8R43 0.20689623 -0.017810079
## c2_F8R44 0.19188223 -0.005231738
## c2_F8R47 0.13202996 0.028771479
## c3_F0R26 -0.15684404 0.031591968
## c3_F0R41 -0.15941698 0.034645181
## c3_F12R32 0.09888443 0.036975231
## c3_F16R31 -0.12521716 0.053371663
## c3_F16R32 0.04194002 0.016550693
## c3_F16R34 -0.01276619 0.043821253
## c3_F16R47 0.12023952 0.005608877
## c3_F21R31 -0.12481360 0.049274411
## c3_F21R35 -0.14360502 0.077179968
## c3_F21R45 0.17029535 0.051021394
## c3_F21R47 0.14805613 -0.003767441
## c3_F8R26 -0.11208391 0.059630870
## c3_F8R27 -0.11426406 0.093938390
## c3_F8R32 0.05714281 0.065830691
## c3_F8R38 0.11585451 0.067736614
## c3_F8R45 0.08574831 0.063020316
## c4_F0R27 -0.08608726 0.092306229
## c4_F0R31 -0.12752825 0.094452333
## c4_F0R32 0.03155450 0.053113921
## c4_F0R46 -0.18477267 0.037913314
## c4_F12R34 -0.03640861 0.131587848
## c4_F12R35 -0.15484668 0.129100846
## c4_F12R36 0.04369001 0.119129368
## c4_F12R41 0.09880819 0.081866740
## c4_F12R46 -0.10952710 0.156867880
## c4_F12R48 -0.16634373 0.078094882
## c4_F16R35 -0.15743694 0.050269920
## c4_F16R41 0.09349854 0.070105660
## c4_F16R46 -0.09214836 0.115829519
## c4_F21R32 0.06360588 0.128503859
## c4_F21R33 0.15782655 0.117936801
## c4_F21R41 0.11902524 0.075693816
## c4_F21R48 -0.10868698 0.128794468
## c4_F8R25 0.13807277 0.063692307
## c4_F8R28 0.17116934 0.036924480
## c4_F8R30 -0.05753295 0.127569399
## c4_F8R33 0.15748532 0.080821868
## c4_F8R37 0.17873534 0.115678451
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL -0.047670297 -0.033135041
## 0_HF_PFOS -0.035137343 -0.080008649
## 12_HF_CTRL -0.014191131 0.065167096
## 12_HF_PFOS 0.006559607 0.041557513
## 16_HF_CTRL -0.027208500 -0.008463845
## 16_HF_PFOS 0.045687920 0.049353052
## 21_HF_CTRL 0.039153793 0.052432931
## 21_HF_PFOS 0.059844554 0.006088934
## 8_HF_CTRL -0.032291139 0.017955631
## 8_HF_PFOS 0.064162699 -0.003527278
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 9 0.007427 0.00082519 0.7116 0.6965
## Residuals 74 0.085807 0.00115955## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 0.4661 0.09180 2.0014 0.002 **
## PFOS 1 0.1022 0.02013 1.7558 0.055 .
## day:PFOS 3 0.1422 0.02801 0.8141 0.805
## Residual 75 4.3665 0.86006
## Total 83 5.0769 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 0.03472408 -0.0699547273
## c1_F0R30 0.18022253 -0.0271653225
## c1_F0R33 -0.22612782 -0.1929873443
## c1_F0R35 0.28796490 -0.1118006854
## c1_F0R36 0.32070254 -0.0710814952
## c1_F0R38 0.23438662 -0.1131692787
## c1_F0R40 0.01733830 -0.0879231762
## c1_F0R42 0.36948352 -0.0963986769
## c1_F0R44 -0.03056405 -0.1026889607
## c1_F0R45 0.35271596 -0.0866032579
## c1_F0R47 0.23880234 -0.0679039011
## c1_F12R33 -0.45268324 -0.3573728931
## c1_F12R42 0.32881911 -0.0811122654
## c1_F16R33 -0.47811267 -0.3688183093
## c1_F16R36 0.02049641 -0.1738445234
## c1_F21R34 0.05921131 0.0211898231
## c1_F21R42 0.16361551 -0.0421669794
## c1_F21R46 0.35306398 -0.0436370243
## c1_F8R29 0.25652512 -0.0458538188
## c1_F8R34 0.23640249 -0.0365543692
## c1_F8R36 0.10296650 0.0215885349
## c1_F8R39 -0.18116716 -0.1635602696
## c1_F8R40 0.25773668 -0.0997395577
## c1_F8R46 0.29045863 -0.0159837246
## c1_F8R48 0.11314541 -0.0164158002
## c2_F0R25 0.10407635 -0.0583558193
## c2_F0R29 0.12493506 0.0868872963
## c2_F0R34 0.22186738 0.0038556561
## c2_F0R37 -0.02855134 -0.0704266652
## c2_F0R39 0.02061350 -0.0854213850
## c2_F0R43 0.23798656 -0.0590521170
## c2_F0R48 -0.11376232 0.1583011233
## c2_F12R31 0.05279865 0.1063146067
## c2_F12R45 -0.06557921 -0.0059609269
## c2_F12R47 -0.48287807 -0.1599926782
## c2_F16R42 0.02159711 0.0921437608
## c2_F16R45 -0.22961613 -0.0732811105
## c2_F16R48 0.21159623 0.0301841965
## c2_F21R36 -0.28421202 0.0085118112
## c2_F8R31 0.33196465 -0.0543957422
## c2_F8R35 0.35985855 -0.0571397624
## c2_F8R41 0.14590193 0.0744270096
## c2_F8R42 -0.20339828 0.2370973981
## c2_F8R43 -0.02596035 -0.0520725081
## c2_F8R44 -0.06869811 -0.0360862415
## c2_F8R47 -0.13289058 -0.0385859439
## c3_F0R26 -0.06493642 0.0175924172
## c3_F0R41 0.28145662 0.0165502804
## c3_F12R32 -0.23476620 0.0215796590
## c3_F16R31 0.03499775 -0.0013090014
## c3_F16R32 0.13963376 -0.0216764379
## c3_F16R34 -0.35615203 0.0572263262
## c3_F16R47 -0.33919466 -0.1484247534
## c3_F21R31 0.08321762 0.0687734114
## c3_F21R35 0.09287813 0.1447648641
## c3_F21R45 -0.37607700 -0.0759445621
## c3_F21R47 -0.33070300 0.0208659274
## c3_F8R26 0.12552961 0.0429357412
## c3_F8R27 -0.04741580 0.1727753038
## c3_F8R32 -0.12797399 0.0758766825
## c3_F8R38 -0.41305965 -0.0009304956
## c3_F8R45 -0.23356694 0.1074798523
## c4_F0R27 0.01623568 0.0780844469
## c4_F0R31 0.07665832 0.0610454649
## c4_F0R32 0.19263180 -0.0205920291
## c4_F0R46 0.26586073 0.0350486796
## c4_F12R34 -0.15701227 0.1292140681
## c4_F12R35 -0.02645609 0.1321281559
## c4_F12R36 -0.15163469 0.1957981714
## c4_F12R41 -0.09825761 0.2167151724
## c4_F12R46 -0.11985308 0.2008736945
## c4_F12R48 0.22544457 0.0168822474
## c4_F16R35 0.24976902 0.0313004561
## c4_F16R41 0.09710938 0.0227050710
## c4_F16R46 -0.06906547 0.2033333885
## c4_F21R32 -0.18202013 0.0498212477
## c4_F21R33 -0.44859052 -0.0373905014
## c4_F21R41 0.05352131 0.0228283324
## c4_F21R48 -0.03060650 0.1849371133
## c4_F8R25 -0.14068861 -0.0394428043
## c4_F8R28 -0.20905080 0.1690201911
## c4_F8R30 -0.24974027 0.1627005714
## c4_F8R33 -0.21755326 -0.0137916547
## c4_F8R37 -0.35834590 0.0836513469
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL 0.125355212 -0.008162345
## 0_HF_PFOS 0.195431433 -0.049461046
## 12_HF_CTRL -0.122482679 0.104497017
## 12_HF_PFOS -0.021177231 0.054566774
## 16_HF_CTRL 0.010698264 -0.053051836
## 16_HF_PFOS -0.008749625 0.049970282
## 21_HF_CTRL -0.077228917 0.051266530
## 21_HF_PFOS 0.003524434 0.020131295
## 8_HF_CTRL 0.053698532 0.030878671
## 8_HF_PFOS -0.065692369 -0.002439797
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 9 0.11458 0.012731 0.8952 0.5339
## Residuals 74 1.05237 0.014221## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 0.8977 0.12263 2.7174 0.009 **
## PFOS 1 0.0340 0.00464 0.4116 0.782
## day:PFOS 3 0.1947 0.02660 0.7858 0.592
## Residual 75 6.1943 0.84613
## Total 83 7.3208 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF_no0 bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F12R33 0.36377727 0.062244669
## c1_F12R42 -0.32571768 -0.181039962
## c1_F16R33 0.39446334 0.091537020
## c1_F16R36 -0.11124179 -0.096309225
## c1_F21R34 -0.14130194 -0.072680591
## c1_F21R42 -0.17609497 -0.147055286
## c1_F21R46 -0.37391713 -0.173669908
## c1_F8R29 -0.32456998 -0.116298336
## c1_F8R34 -0.26583446 -0.136884065
## c1_F8R36 -0.18544742 -0.094344029
## c1_F8R39 0.14729714 -0.013974943
## c1_F8R40 -0.23909482 -0.222557156
## c1_F8R46 -0.34617958 -0.158865129
## c1_F8R48 -0.21733951 -0.084292474
## c2_F12R31 -0.27327946 0.089198401
## c2_F12R45 0.01913537 -0.051447854
## c2_F12R47 0.42782094 0.049800578
## c2_F16R42 -0.17185722 0.065065236
## c2_F16R45 0.29368612 -0.019756273
## c2_F16R48 -0.33802524 0.002301164
## c2_F21R36 0.32768348 0.035933775
## c2_F8R31 -0.33844160 -0.146874377
## c2_F8R35 -0.36059391 -0.154470845
## c2_F8R41 -0.15098340 -0.140405272
## c2_F8R42 0.01220291 0.316513314
## c2_F8R43 0.37787573 -0.186139181
## c2_F8R44 0.39648808 -0.185026546
## c2_F8R47 0.20904740 -0.057824487
## c3_F12R32 0.32311588 -0.037768744
## c3_F16R31 -0.18270060 0.052117893
## c3_F16R32 -0.08758392 -0.150139599
## c3_F16R34 0.21986941 0.281402775
## c3_F16R47 0.27470802 0.095377937
## c3_F21R31 -0.24313212 0.060572963
## c3_F21R35 -0.31409875 0.138252956
## c3_F21R45 0.47498468 -0.062593503
## c3_F21R47 0.41714451 -0.093599976
## c3_F8R26 -0.26296151 0.007305451
## c3_F8R27 -0.11720495 0.211179424
## c3_F8R32 0.26652929 -0.061204856
## c3_F8R38 0.46344618 -0.029268304
## c3_F8R45 0.25530288 0.001485033
## c4_F12R34 -0.05906675 0.258522696
## c4_F12R35 -0.26262335 0.205281435
## c4_F12R36 -0.09489015 0.281974956
## c4_F12R41 0.02332875 -0.091226026
## c4_F12R46 -0.15631290 0.287238419
## c4_F12R48 -0.33371745 -0.026248712
## c4_F16R35 -0.37589337 -0.001209486
## c4_F16R41 -0.08814973 -0.187675556
## c4_F16R46 -0.21707029 0.260767052
## c4_F21R32 0.25104919 -0.031568030
## c4_F21R33 0.37894012 0.197788772
## c4_F21R41 0.01014646 -0.113700551
## c4_F21R48 -0.26452505 0.232423286
## c4_F8R25 0.06372991 -0.005821609
## c4_F8R28 0.37781774 -0.194861311
## c4_F8R30 -0.06656990 0.335800102
## c4_F8R33 0.26158390 0.001770667
## c4_F8R37 0.43524623 -0.095053773
##
## $centroids
## PCoA1 PCoA2
## 12_HF_CTRL -0.082684344 0.182534996
## 12_HF_PFOS -0.098658410 -0.007503936
## 16_HF_CTRL -0.092956825 0.010193723
## 16_HF_PFOS -0.101332980 0.037355919
## 21_HF_CTRL 0.009774241 0.047608649
## 21_HF_PFOS -0.049975593 -0.070611130
## 8_HF_CTRL -0.143334693 -0.042703094
## 8_HF_PFOS 0.113634634 -0.075430131
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.03535 0.0050501 0.2476 0.9708
## Residuals 52 1.06063 0.0203967## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 3 0.5897 0.05449 1.0741 0.339
## PFOS 1 0.2660 0.02458 1.4533 0.178
## day:PFOS 3 0.4501 0.04159 0.8198 0.654
## Residual 52 9.5168 0.87935
## Total 59 10.8226 1.00000
## [1] ""
## [1] "Processing Feces_HF_no0 jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F12R33 0.07700312 -0.328803210
## c1_F12R42 0.29500462 -0.101425833
## c1_F16R33 0.08275981 -0.314050781
## c1_F16R36 0.13925666 -0.271387948
## c1_F21R34 0.16293244 -0.268270523
## c1_F21R42 0.16628603 -0.248280462
## c1_F21R46 0.33737933 -0.046868973
## c1_F8R29 0.31347656 -0.117464895
## c1_F8R34 0.26321386 -0.149580567
## c1_F8R36 0.26461968 -0.157078396
## c1_F8R39 0.09528989 -0.304002558
## c1_F8R40 0.11931054 -0.294109213
## c1_F8R46 0.31828719 -0.065830662
## c1_F8R48 0.23937905 -0.166075924
## c2_F12R31 0.11535861 0.134533121
## c2_F12R45 -0.14631823 -0.079030866
## c2_F12R47 -0.21212548 -0.099901923
## c2_F16R42 -0.05741079 -0.020645422
## c2_F16R45 -0.18180413 -0.095146089
## c2_F16R48 0.14494159 0.148379228
## c2_F21R36 -0.15923191 -0.063855775
## c2_F8R31 0.09826364 0.128830957
## c2_F8R35 0.17210238 0.178281299
## c2_F8R41 -0.01509871 -0.001950968
## c2_F8R42 0.04976449 0.097464880
## c2_F8R43 -0.22088293 -0.169292590
## c2_F8R44 -0.19831621 -0.136330799
## c2_F8R47 -0.15299213 -0.079348490
## c3_F12R32 -0.14801888 0.007803348
## c3_F16R31 0.05781366 0.158656562
## c3_F16R32 -0.11125867 0.048781783
## c3_F16R34 -0.07930575 0.051288780
## c3_F16R47 -0.21402120 -0.039669177
## c3_F21R31 0.07266434 0.186366866
## c3_F21R35 0.09375643 0.207553201
## c3_F21R45 -0.25702540 -0.051209454
## c3_F21R47 -0.23017857 -0.065402226
## c3_F8R26 0.08195326 0.176792849
## c3_F8R27 0.01557175 0.163815180
## c3_F8R32 -0.14542769 0.029547677
## c3_F8R38 -0.20643430 -0.024124339
## c3_F8R45 -0.19175605 0.014531858
## c4_F12R34 0.03525964 0.168112937
## c4_F12R35 0.14100428 0.219959132
## c4_F12R36 -0.02138262 0.131943724
## c4_F12R41 -0.18665034 0.009102174
## c4_F12R46 0.11640002 0.229872684
## c4_F12R48 0.11685846 0.235578663
## c4_F16R35 0.15190478 0.234891704
## c4_F16R41 -0.17678842 0.063148850
## c4_F16R46 0.11314035 0.251079210
## c4_F21R32 -0.13363242 0.059780541
## c4_F21R33 -0.15500173 0.032735669
## c4_F21R41 -0.15555529 0.022751870
## c4_F21R48 0.10509007 0.225940512
## c4_F8R25 -0.19671443 0.016832947
## c4_F8R28 -0.20230665 -0.013239523
## c4_F8R30 0.02345126 0.166222773
## c4_F8R33 -0.16944824 -0.014697378
## c4_F8R37 -0.25441065 -0.013506016
##
## $centroids
## PCoA1 PCoA2
## 12_HF_CTRL 0.038949412 0.085372808
## 12_HF_PFOS -0.005880226 0.042551094
## 16_HF_CTRL 0.034072022 -0.009464575
## 16_HF_PFOS -0.064573611 0.043869516
## 21_HF_CTRL -0.033849923 0.030891941
## 21_HF_PFOS -0.009101725 -0.027823973
## 8_HF_CTRL 0.045458806 0.032418800
## 8_HF_PFOS -0.045525832 -0.095197401
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.00927 0.0013243 0.6412 0.7198
## Residuals 52 0.10741 0.0020655## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 3 0.4709 0.04741 0.9317 0.631
## PFOS 1 0.3053 0.03074 1.8119 0.036 *
## day:PFOS 3 0.3946 0.03973 0.7807 0.892
## Residual 52 8.7615 0.88212
## Total 59 9.9324 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF_no0 unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F12R33 0.124945743 0.189703420
## c1_F12R42 -0.156535740 0.120281259
## c1_F16R33 0.078677070 0.190708901
## c1_F16R36 0.035542320 0.157399101
## c1_F21R34 0.026542936 0.154657059
## c1_F21R42 0.032476565 0.175272038
## c1_F21R46 -0.147040707 0.114777516
## c1_F8R29 -0.104192684 0.137542834
## c1_F8R34 -0.130690871 0.154920025
## c1_F8R36 -0.103927732 0.114637545
## c1_F8R39 0.058487334 0.147456198
## c1_F8R40 0.004299051 0.149936230
## c1_F8R46 -0.176926507 0.092507145
## c1_F8R48 -0.086489547 0.130160896
## c2_F12R31 -0.132425252 -0.063898758
## c2_F12R45 0.123644209 -0.021288579
## c2_F12R47 0.137277275 -0.034451720
## c2_F16R42 0.060590624 -0.035679593
## c2_F16R45 0.152949702 -0.016355029
## c2_F16R48 -0.130726364 -0.031499403
## c2_F21R36 0.110833851 -0.026496544
## c2_F8R31 -0.140790767 -0.028566865
## c2_F8R35 -0.204674074 -0.032533928
## c2_F8R41 0.022889309 -0.005447177
## c2_F8R42 -0.046574218 -0.047218941
## c2_F8R43 0.173910998 0.029310107
## c2_F8R44 0.134870692 0.014227259
## c2_F8R47 0.081224581 -0.006801559
## c3_F12R32 0.049184771 -0.039776945
## c3_F16R31 -0.137214824 -0.059311298
## c3_F16R32 0.044140532 0.016231663
## c3_F16R34 0.012342756 -0.012689490
## c3_F16R47 0.092554052 0.014121646
## c3_F21R31 -0.169510916 -0.068510202
## c3_F21R35 -0.152867439 -0.080488294
## c3_F21R45 0.151853434 -0.023107271
## c3_F21R47 0.128020457 0.028453545
## c3_F8R26 -0.119716385 0.009802263
## c3_F8R27 -0.045155404 -0.026596480
## c3_F8R32 0.059399174 -0.001232687
## c3_F8R38 0.116298743 -0.065659003
## c3_F8R45 0.091898452 -0.087421242
## c4_F12R34 -0.051790960 -0.053330856
## c4_F12R35 -0.134363467 -0.063135016
## c4_F12R36 -0.023445480 -0.060906687
## c4_F12R41 0.114211063 -0.071242851
## c4_F12R46 -0.100471528 -0.119759595
## c4_F12R48 -0.118625341 -0.095788481
## c4_F16R35 -0.173254665 -0.056342849
## c4_F16R41 0.100663017 -0.061828024
## c4_F16R46 -0.153903529 -0.116207657
## c4_F21R32 0.034501320 -0.081092877
## c4_F21R33 0.124283626 -0.069410266
## c4_F21R41 0.095003732 -0.035825299
## c4_F21R48 -0.117153746 -0.086610445
## c4_F8R25 0.141170151 -0.088838705
## c4_F8R28 0.134773966 -0.047723994
## c4_F8R30 -0.080863359 -0.085177316
## c4_F8R33 0.146084049 -0.047174875
## c4_F8R37 0.143785955 -0.086679847
##
## $centroids
## PCoA1 PCoA2
## 12_HF_CTRL -0.041905387 -0.03154221
## 12_HF_PFOS -0.001466703 -0.04442774
## 16_HF_CTRL -0.015794080 0.04401606
## 16_HF_PFOS 0.030243219 -0.03911177
## 21_HF_CTRL 0.007668443 -0.03113829
## 21_HF_PFOS 0.027592245 0.03243070
## 8_HF_CTRL -0.044741281 0.01146677
## 8_HF_PFOS 0.049615915 0.01908735
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.002956 0.00042232 0.316 0.9435
## Residuals 52 0.069503 0.00133660## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 3 0.1395 0.04347 0.8528 0.706
## PFOS 1 0.0933 0.02907 1.7107 0.062 .
## day:PFOS 3 0.1410 0.04394 0.8620 0.695
## Residual 52 2.8350 0.88353
## Total 59 3.2087 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF_no0 wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F12R33 0.431858126 -0.3459518060
## c1_F12R42 -0.367898927 -0.1179206134
## c1_F16R33 0.454555895 -0.3642714578
## c1_F16R36 -0.062097852 -0.1903685178
## c1_F21R34 -0.123272523 -0.0008815405
## c1_F21R42 -0.214694557 -0.0629174779
## c1_F21R46 -0.398961614 -0.0998596282
## c1_F8R29 -0.305406914 -0.1026801457
## c1_F8R34 -0.286927410 -0.0873258012
## c1_F8R36 -0.165381018 -0.0210809783
## c1_F8R39 0.133673435 -0.1739258093
## c1_F8R40 -0.297972062 -0.1266656965
## c1_F8R46 -0.344039233 -0.0738454428
## c1_F8R48 -0.175505066 -0.0657078817
## c2_F12R31 -0.113420859 0.0713522616
## c2_F12R45 0.013549475 -0.0073182583
## c2_F12R47 0.447168782 -0.1758534674
## c2_F16R42 -0.077743431 0.0794454320
## c2_F16R45 0.180788586 -0.0588109275
## c2_F16R48 -0.260624632 -0.0117239181
## c2_F21R36 0.231884953 0.0227719195
## c2_F8R31 -0.369635958 -0.0912043433
## c2_F8R35 -0.397591324 -0.0942306316
## c2_F8R41 -0.196911077 0.0566674046
## c2_F8R42 0.138202157 0.2093781079
## c2_F8R43 -0.022930954 -0.0404186761
## c2_F8R44 0.018137540 -0.0187962347
## c2_F8R47 0.083837682 -0.0401654454
## c3_F12R32 0.182084186 0.0482842887
## c3_F16R31 -0.091441134 -0.0434844711
## c3_F16R32 -0.186249193 -0.0289539580
## c3_F16R34 0.302939239 0.0373304080
## c3_F16R47 0.298784377 -0.1613847493
## c3_F21R31 -0.142534594 0.0253943141
## c3_F21R35 -0.156839814 0.1039854031
## c3_F21R45 0.334175081 -0.0511872659
## c3_F21R47 0.280348036 0.0427771192
## c3_F8R26 -0.175157680 0.0050563737
## c3_F8R27 -0.013725803 0.1790625864
## c3_F8R32 0.073113803 0.1023042035
## c3_F8R38 0.368344684 0.0362603887
## c3_F8R45 0.175970992 0.0981807004
## c4_F12R34 0.095167488 0.1080946542
## c4_F12R35 -0.037448252 0.0992799807
## c4_F12R36 0.085101346 0.1773307001
## c4_F12R41 0.040721531 0.2336436440
## c4_F12R46 0.048982496 0.1695996723
## c4_F12R48 -0.272666565 -0.0220256908
## c4_F16R35 -0.299756125 -0.0211989789
## c4_F16R41 -0.144891183 0.0309708546
## c4_F16R46 -0.004556173 0.1612556654
## c4_F21R32 0.125538595 0.0626288507
## c4_F21R33 0.397255037 -0.0545462443
## c4_F21R41 -0.103618904 0.0277484118
## c4_F21R48 -0.038238727 0.1517684349
## c4_F8R25 0.091654334 -0.0455318413
## c4_F8R28 0.152115105 0.2040573195
## c4_F8R30 0.188663880 0.1434563755
## c4_F8R33 0.167689760 -0.0055790185
## c4_F8R37 0.305832959 0.1177314429
##
## $centroids
## PCoA1 PCoA2
## 12_HF_CTRL 0.06406113 0.087805172
## 12_HF_PFOS -0.02920955 0.042006998
## 16_HF_CTRL -0.05863220 -0.081106925
## 16_HF_PFOS -0.04379929 0.035294408
## 21_HF_CTRL 0.02011531 0.034608323
## 21_HF_PFOS -0.05542331 0.009810830
## 8_HF_CTRL -0.10452464 0.010433478
## 8_HF_PFOS 0.01531138 -0.007720369
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.03441 0.0049161 0.3118 0.9454
## Residuals 52 0.81984 0.0157662## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 3 0.2483 0.04514 0.8568 0.543
## PFOS 1 0.0340 0.00618 0.3519 0.856
## day:PFOS 3 0.1947 0.03539 0.6718 0.725
## Residual 52 5.0237 0.91328
## Total 59 5.5007 1.00000
## [1] ""
## [1] "Processing Feces_HF_d08 bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 0.252765333 -0.121621588
## c1_F0R30 -0.232289382 -0.028975042
## c1_F0R33 0.151039742 0.022468589
## c1_F0R35 -0.211874739 -0.181393553
## c1_F0R36 -0.306340545 -0.079458520
## c1_F0R38 -0.098798935 -0.180187464
## c1_F0R40 0.156749354 -0.097905101
## c1_F0R42 -0.321519256 -0.112310895
## c1_F0R44 -0.062014054 0.058268060
## c1_F0R45 -0.304778121 -0.110012522
## c1_F0R47 -0.223200812 -0.149052749
## c1_F8R29 -0.256781549 -0.036978953
## c1_F8R34 -0.164446425 -0.050780697
## c1_F8R36 -0.070725501 -0.001529316
## c1_F8R39 0.217348110 0.042231359
## c1_F8R40 -0.146374699 -0.130733144
## c1_F8R46 -0.248586296 -0.053252819
## c1_F8R48 -0.093073409 0.035943618
## c2_F0R25 -0.055850624 -0.070351267
## c2_F0R29 -0.239939557 0.121754155
## c2_F0R34 -0.208201613 0.021447551
## c2_F0R37 0.104660553 -0.081493991
## c2_F0R39 -0.002013703 0.005639187
## c2_F0R43 -0.113213210 -0.174028103
## c2_F0R48 -0.004237325 0.276782830
## c2_F8R31 -0.284422317 -0.069633402
## c2_F8R35 -0.291240729 -0.065481970
## c2_F8R41 -0.036769235 -0.036731981
## c2_F8R42 0.184315754 0.371499319
## c2_F8R43 0.495819848 -0.176055536
## c2_F8R44 0.514067873 -0.179107227
## c2_F8R47 0.306347866 0.012124354
## c3_F0R26 -0.125612107 0.198366753
## c3_F0R41 -0.317564691 -0.029306481
## c3_F8R26 -0.182171631 0.120380291
## c3_F8R27 0.066943487 0.267928043
## c3_F8R32 0.394715631 0.030124413
## c3_F8R38 0.515828521 -0.013043617
## c3_F8R45 0.345428714 0.103916129
## c4_F0R27 -0.130776986 0.180015853
## c4_F0R31 -0.146608286 0.111336400
## c4_F0R32 -0.139058950 -0.081290373
## c4_F0R46 -0.302679122 0.062426382
## c4_F8R25 0.151692082 0.075151983
## c4_F8R28 0.514468638 -0.167241742
## c4_F8R30 0.058910697 0.412408919
## c4_F8R33 0.348670026 0.045239358
## c4_F8R37 0.541391579 -0.097495492
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL -0.15331253 0.01084644
## 0_HF_PFOS -0.15255208 -0.06509673
## 8_HF_CTRL -0.04688672 0.03702444
## 8_HF_PFOS 0.21676613 -0.01134710
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.18412 0.061372 4.7919 0.00565 **
## Residuals 44 0.56353 0.012808
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.8762 0.12187 6.5798 0.002 **
## PFOS 1 0.3212 0.04467 2.4120 0.043 *
## Residual 45 5.9928 0.83346
## Total 47 7.1902 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF_d08 jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 0.107405433 -0.2827883234
## c1_F0R30 0.304135493 0.0032014573
## c1_F0R33 0.151661343 -0.1963834284
## c1_F0R35 0.132885598 -0.2556910143
## c1_F0R36 0.276032260 0.0634336797
## c1_F0R38 0.164916734 -0.1962269758
## c1_F0R40 0.084888150 -0.2748737511
## c1_F0R42 0.288466866 0.0034438162
## c1_F0R44 0.255206444 -0.0007392761
## c1_F0R45 0.283221339 0.0346298550
## c1_F0R47 0.127355283 -0.2158528818
## c1_F8R29 0.261646942 0.0179233298
## c1_F8R34 0.220881446 -0.0554177517
## c1_F8R36 0.262472914 -0.0194659770
## c1_F8R39 0.131767346 -0.2120678610
## c1_F8R40 0.133410949 -0.2246417829
## c1_F8R46 0.284556989 0.0290392269
## c1_F8R48 0.244182044 -0.0258393754
## c2_F0R25 -0.220023705 -0.1350118090
## c2_F0R29 -0.006051637 0.2217936059
## c2_F0R34 -0.048536419 0.1443916955
## c2_F0R37 -0.196369179 -0.1212887744
## c2_F0R39 -0.178986043 -0.0044807712
## c2_F0R43 -0.183940951 -0.1337041786
## c2_F0R48 -0.051406976 0.2265096345
## c2_F8R31 0.018920932 0.1871139682
## c2_F8R35 0.035785526 0.2153705938
## c2_F8R41 -0.105482552 0.0421198313
## c2_F8R42 -0.077659317 0.1577465632
## c2_F8R43 -0.246984492 -0.2145568075
## c2_F8R44 -0.234270383 -0.1826730476
## c2_F8R47 -0.210473585 -0.0989008321
## c3_F0R26 -0.023141124 0.2845279843
## c3_F0R41 0.033214552 0.2392394056
## c3_F8R26 -0.004233252 0.2778768792
## c3_F8R27 -0.058843996 0.2013283513
## c3_F8R32 -0.170106118 0.0399901163
## c3_F8R38 -0.204846088 -0.0041256314
## c3_F8R45 -0.206548560 -0.0113451604
## c4_F0R27 -0.110455891 0.1648601951
## c4_F0R31 -0.072076410 0.1807269220
## c4_F0R32 -0.150364594 0.0369722402
## c4_F0R46 0.073236629 0.2441833751
## c4_F8R25 -0.239552549 -0.0705842621
## c4_F8R28 -0.242123031 -0.0904182180
## c4_F8R30 -0.069172068 0.2076792161
## c4_F8R33 -0.256190477 -0.0814008769
## c4_F8R37 -0.308411814 -0.1156231741
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL 0.02490708 0.02524772
## 0_HF_PFOS 0.07418342 -0.02489793
## 8_HF_CTRL -0.01376580 0.07227901
## 8_HF_PFOS -0.08035468 -0.07466553
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.001254 0.00041814 0.2802 0.8394
## Residuals 44 0.065672 0.00149253## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.3501 0.04330 2.1054 0.020 *
## PFOS 1 0.2526 0.03125 1.5193 0.088 .
## Residual 45 7.4824 0.92546
## Total 47 8.0851 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF_d08 unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 0.068046966 -0.170554712
## c1_F0R30 -0.144028771 -0.134132008
## c1_F0R33 0.022035875 -0.159311591
## c1_F0R35 0.048220591 -0.152300741
## c1_F0R36 -0.189263257 -0.058385934
## c1_F0R38 -0.017329855 -0.169413730
## c1_F0R40 0.080201745 -0.150537756
## c1_F0R42 -0.136591081 -0.102746428
## c1_F0R44 -0.122489078 -0.094634825
## c1_F0R45 -0.154125620 -0.086736207
## c1_F0R47 0.025978984 -0.183881340
## c1_F8R29 -0.126809913 -0.066893531
## c1_F8R34 -0.111339519 -0.082672232
## c1_F8R36 -0.118633588 -0.046350814
## c1_F8R39 0.045195159 -0.102459864
## c1_F8R40 -0.006139733 -0.126329721
## c1_F8R46 -0.125311091 -0.043668222
## c1_F8R48 -0.123389849 -0.075916231
## c2_F0R25 0.155622893 -0.006945556
## c2_F0R29 -0.106009912 0.113632850
## c2_F0R34 -0.031239917 0.068597646
## c2_F0R37 0.179541603 0.026719874
## c2_F0R39 0.099777396 0.013230664
## c2_F0R43 0.158759724 -0.041838351
## c2_F0R48 -0.124822677 0.118245473
## c2_F8R31 -0.137208651 0.040080565
## c2_F8R35 -0.136251457 0.090805344
## c2_F8R41 0.045082522 0.056121407
## c2_F8R42 -0.013029443 0.122828490
## c2_F8R43 0.202215859 -0.023515756
## c2_F8R44 0.194721970 -0.001524607
## c2_F8R47 0.128642657 0.021978071
## c3_F0R26 -0.136611469 0.110773460
## c3_F0R41 -0.169124234 0.107800319
## c3_F8R26 -0.099685316 0.122825744
## c3_F8R27 -0.034302310 0.077617991
## c3_F8R32 0.077204822 0.058458671
## c3_F8R38 0.127595348 0.072222244
## c3_F8R45 0.146836909 0.061468665
## c4_F0R27 -0.056131583 0.138157854
## c4_F0R31 -0.073227696 0.176949901
## c4_F0R32 0.088481509 0.067373122
## c4_F0R46 -0.130432486 0.097285561
## c4_F8R25 0.182812753 0.062848586
## c4_F8R28 0.178197721 0.031942922
## c4_F8R30 -0.057847787 0.108160744
## c4_F8R33 0.197807875 0.051815827
## c4_F8R37 0.228395414 0.062808163
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL -0.03358752 0.005808993
## 0_HF_PFOS -0.03086223 -0.052164142
## 8_HF_CTRL -0.02776594 0.037128111
## 8_HF_PFOS 0.08186332 0.004532490
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.002523 0.0008410 0.6674 0.5766
## Residuals 44 0.055448 0.0012602## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.17294 0.06022 2.9757 0.007 **
## PFOS 1 0.08364 0.02912 1.4392 0.137
## Residual 45 2.61539 0.91066
## Total 47 2.87198 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF_d08 wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 -0.05068691 0.205185917
## c1_F0R30 0.13597715 -0.027695499
## c1_F0R33 -0.23550475 0.146201798
## c1_F0R35 0.23456985 0.098953721
## c1_F0R36 0.28166916 -0.022865466
## c1_F0R38 0.16958947 0.158805516
## c1_F0R40 -0.05435471 0.184397664
## c1_F0R42 0.33106766 0.007396747
## c1_F0R44 -0.05933443 0.040009126
## c1_F0R45 0.31372890 -0.002106722
## c1_F0R47 0.18979872 0.016541232
## c1_F8R29 0.21243236 -0.045929004
## c1_F8R34 0.18565064 -0.031862506
## c1_F8R36 0.03670494 -0.034949119
## c1_F8R39 -0.20287898 0.120338023
## c1_F8R40 0.21090834 0.054378711
## c1_F8R46 0.23558093 -0.057929152
## c1_F8R48 0.05495958 -0.029666908
## c2_F0R25 0.05355123 0.041495553
## c2_F0R29 0.05990130 -0.118695826
## c2_F0R34 0.16894274 -0.058065222
## c2_F0R37 -0.08641611 0.144900077
## c2_F0R39 -0.01833721 0.048255725
## c2_F0R43 0.18372423 0.039462721
## c2_F0R48 -0.18641229 -0.181680990
## c2_F8R31 0.28649757 -0.011951679
## c2_F8R35 0.31267428 -0.010529609
## c2_F8R41 0.07297087 -0.055576189
## c2_F8R42 -0.27951389 -0.276307554
## c2_F8R43 -0.09511724 0.128967030
## c2_F8R44 -0.14058035 0.130704225
## c2_F8R47 -0.18272443 0.061212966
## c3_F0R26 -0.11282453 -0.052545845
## c3_F0R41 0.23000968 -0.075314737
## c3_F8R26 0.07032954 -0.100887981
## c3_F8R27 -0.14764288 -0.072868810
## c3_F8R32 -0.21794498 0.049159611
## c3_F8R38 -0.45980717 0.055341741
## c3_F8R45 -0.29885112 -0.111150812
## c4_F0R27 -0.05232202 -0.063664315
## c4_F0R31 0.01070849 -0.067672831
## c4_F0R32 0.13398266 0.003711342
## c4_F0R46 0.21186589 -0.095786144
## c4_F8R25 -0.18947330 0.048758815
## c4_F8R28 -0.30565056 -0.024988825
## c4_F8R30 -0.31417432 -0.196572406
## c4_F8R33 -0.26950108 0.038116510
## c4_F8R37 -0.42774291 0.004969380
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL 0.071935410 -0.01366262
## 0_HF_PFOS 0.147998918 0.01817669
## 8_HF_CTRL -0.007478831 -0.03645230
## 8_HF_PFOS -0.125239264 0.02244024
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.06829 0.022763 2.5852 0.06513 .
## Residuals 44 0.38742 0.008805
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.3361 0.09448 4.8219 0.01 **
## PFOS 1 0.0845 0.02375 1.2118 0.27
## Residual 45 3.1371 0.88177
## Total 47 3.5577 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 0.34778574 -0.086587290
## c1_F0R06 -0.02680685 -0.315875844
## c1_F0R07 0.50839605 -0.096636086
## c1_F0R08 0.01746118 -0.376048616
## c1_F0R09 -0.14215062 -0.346056924
## c1_F0R12 0.16816177 -0.140255074
## c1_F0R14 0.23355856 -0.138542623
## c1_F0R15 0.18527261 -0.138977982
## c1_F0R24 0.01200033 -0.348863557
## c1_F12R09 0.27350228 0.092600094
## c1_F12R19 -0.18992656 -0.322519970
## c1_F16R08 0.37827320 -0.071036170
## c1_F16R20 0.13097477 -0.167267312
## c1_F16R21 0.30949942 0.006625188
## c1_F16R22 0.18052526 -0.060509073
## c1_F21R19 -0.14871977 -0.212551815
## c1_F21R23 -0.03375660 -0.002118749
## c1_F8R09 -0.11023258 -0.200979460
## c1_F8R12 0.32376102 -0.055316674
## c1_F8R17 0.09734761 0.116618719
## c1_F8R18 -0.10305744 -0.185203950
## c1_F8R22 0.04474433 -0.328493474
## c2_F0R01 0.10090987 -0.061879848
## c2_F0R05 0.18948328 0.012331058
## c2_F0R13 -0.02308769 -0.078476897
## c2_F0R17 0.12096953 -0.035860455
## c2_F0R18 0.17172145 -0.179994339
## c2_F0R19 -0.02592274 -0.263114402
## c2_F0R20 -0.09582053 -0.167361268
## c2_F12R07 -0.06481371 0.019340876
## c2_F12R23 -0.16771927 0.163515806
## c2_F16R19 -0.25563732 -0.159075922
## c2_F21R10 -0.01776302 -0.081813482
## c2_F21R20 -0.08877290 0.173653481
## c2_F21R21 -0.05476779 0.140357311
## c2_F21R24 -0.25915299 -0.042984832
## c2_F8R02 -0.01593326 0.053539005
## c2_F8R16 -0.24950302 -0.170708063
## c2_F8R20 0.01931709 0.057574662
## c3_F0R16 -0.25997044 -0.099789146
## c3_F0R21 0.16850049 0.254166620
## c3_F0R23 -0.12952849 0.120155258
## c3_F12R08 0.36461889 0.045165768
## c3_F12R10 -0.13859526 0.037305794
## c3_F12R11 -0.11949358 -0.016081562
## c3_F12R20 -0.27172390 -0.130815458
## c3_F12R21 -0.09685839 0.280471457
## c3_F12R22 -0.06564768 0.225268228
## c3_F16R07 0.13079186 0.124609232
## c3_F16R11 0.12264404 0.035149995
## c3_F16R12 0.09540312 0.294359723
## c3_F16R23 -0.20655966 0.187630605
## c3_F21R09 0.05730734 0.088644702
## c3_F21R12 -0.23110202 0.013401462
## c3_F21R22 -0.20033029 0.190357875
## c3_F8R04 -0.01357217 0.207969174
## c3_F8R06 -0.16553943 -0.129079752
## c3_F8R07 0.14073321 0.275803560
## c3_F8R10 0.05741547 0.179966427
## c3_F8R11 -0.15455702 0.113855651
## c3_F8R13 -0.13608721 0.086314426
## c3_F8R14 -0.23514161 -0.048246791
## c3_F8R19 -0.18958839 0.191141778
## c3_F8R23 -0.23667738 0.191146133
## c3_F8R24 -0.08076378 -0.009735374
## c4_F0R02 -0.07726023 0.136078623
## c4_F0R03 0.11306301 0.056290874
## c4_F0R10 0.35065676 0.100467782
## c4_F0R11 0.07873589 -0.226776493
## c4_F0R22 0.04407429 0.143636781
## c4_F12R12 -0.07708368 0.152526506
## c4_F12R24 -0.16177989 0.107284762
## c4_F16R09 -0.12527257 0.096282752
## c4_F16R10 0.01924880 0.170601663
## c4_F16R24 -0.06543655 0.252410163
## c4_F21R07 0.26214988 0.075591805
## c4_F21R08 0.35419577 0.061912511
## c4_F21R11 -0.15778704 0.180839576
## c4_F8R01 -0.25274544 -0.230944438
## c4_F8R03 -0.18071608 0.056848042
## c4_F8R05 -0.05902083 0.168839993
## c4_F8R08 0.16257527 -0.146332482
## c4_F8R15 -0.20048550 -0.019542155
## c4_F8R21 0.02708974 0.153801900
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL 1.420487e-01 -0.10814929
## 0_LF_PFOS 3.456069e-02 -0.08860081
## 12_LF_CTRL -9.987074e-05 0.05579651
## 12_LF_PFOS -1.548449e-01 0.08060055
## 16_LF_CTRL 9.612976e-02 0.11951483
## 16_LF_PFOS 1.664053e-02 0.01958993
## 21_LF_CTRL 5.600739e-02 0.05603590
## 21_LF_PFOS -1.375988e-01 0.04402525
## 8_LF_CTRL -2.624296e-02 0.03927987
## 8_LF_PFOS -1.132738e-01 0.01308794
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 9 0.03122 0.0034691 0.4791 0.8842
## Residuals 74 0.53583 0.0072409## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 1.6716 0.12363 2.8212 0.001 ***
## PFOS 1 0.4148 0.03068 2.8004 0.005 **
## day:PFOS 3 0.3254 0.02406 0.7322 0.904
## Residual 75 11.1095 0.82163
## Total 83 13.5213 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 -0.306087293 -0.08023479
## c1_F0R06 -0.274964535 -0.03376266
## c1_F0R07 -0.323395933 -0.05776872
## c1_F0R08 -0.294502917 -0.03202889
## c1_F0R09 -0.283370945 -0.04170233
## c1_F0R12 -0.301650845 -0.05332599
## c1_F0R14 -0.305668704 -0.04752387
## c1_F0R15 -0.300457834 -0.06511641
## c1_F0R24 -0.295883557 -0.02686986
## c1_F12R09 -0.263240343 -0.05590429
## c1_F12R19 -0.270984959 -0.03823488
## c1_F16R08 -0.252735094 -0.04090427
## c1_F16R20 -0.270978614 -0.05605933
## c1_F16R21 -0.285080642 -0.04986390
## c1_F16R22 -0.262919341 -0.03798182
## c1_F21R19 -0.274113538 -0.03990325
## c1_F21R23 -0.274813483 -0.04274365
## c1_F8R09 -0.283479717 -0.03694780
## c1_F8R12 -0.283049316 -0.05813097
## c1_F8R17 -0.267104536 -0.07779834
## c1_F8R18 -0.266827278 -0.02550911
## c1_F8R22 -0.285710915 -0.02668530
## c2_F0R01 0.006968392 0.08020955
## c2_F0R05 0.001615050 0.07803791
## c2_F0R13 0.022243593 0.06344756
## c2_F0R17 -0.014707788 0.07897502
## c2_F0R18 0.038603463 0.06818340
## c2_F0R19 0.015501301 0.06553439
## c2_F0R20 0.013321267 0.08438492
## c2_F12R07 0.006248914 0.07187731
## c2_F12R23 0.027974538 0.05132500
## c2_F16R19 0.003716084 0.06037742
## c2_F21R10 0.026090841 0.11185166
## c2_F21R20 0.073007515 0.07945115
## c2_F21R21 0.054191971 0.07537794
## c2_F21R24 0.041525115 0.11301014
## c2_F8R02 0.040609858 0.09027295
## c2_F8R16 -0.002476403 0.10028167
## c2_F8R20 0.017554697 0.07609208
## c3_F0R16 0.126957538 -0.16359868
## c3_F0R21 0.157789025 -0.14164281
## c3_F0R23 0.142253540 -0.17779487
## c3_F12R08 0.133092007 -0.16172092
## c3_F12R10 0.173682477 -0.16291079
## c3_F12R11 0.144321121 -0.14410718
## c3_F12R20 0.157443519 -0.15733716
## c3_F12R21 0.154547605 -0.16466380
## c3_F12R22 0.185191700 -0.15372329
## c3_F16R07 0.169683805 -0.14701516
## c3_F16R11 0.167543305 -0.16723648
## c3_F16R12 0.158083422 -0.14874889
## c3_F16R23 0.178092331 -0.18111710
## c3_F21R09 0.178045379 -0.15385849
## c3_F21R12 0.162628701 -0.16700505
## c3_F21R22 0.208406354 -0.17677800
## c3_F8R04 0.157095479 -0.14487307
## c3_F8R06 0.153217127 -0.17268238
## c3_F8R07 0.155038856 -0.16345856
## c3_F8R10 0.120680112 -0.15573446
## c3_F8R11 0.188380526 -0.14228451
## c3_F8R13 0.148524258 -0.17797699
## c3_F8R14 0.152932079 -0.17851363
## c3_F8R19 0.172124065 -0.17035493
## c3_F8R23 0.133520155 -0.16996274
## c3_F8R24 0.172673175 -0.17431683
## c4_F0R02 0.069764266 0.18988788
## c4_F0R03 0.032562193 0.15442374
## c4_F0R10 0.044589028 0.22439953
## c4_F0R11 0.085512162 0.20504083
## c4_F0R22 0.072323040 0.21827976
## c4_F12R12 0.094814471 0.19157800
## c4_F12R24 0.086873567 0.19573723
## c4_F16R09 0.102977947 0.22605128
## c4_F16R10 0.128605372 0.22579314
## c4_F16R24 0.138392617 0.17290652
## c4_F21R07 0.120219380 0.21221119
## c4_F21R08 0.114223530 0.22362356
## c4_F21R11 0.115872494 0.19839571
## c4_F8R01 0.066825621 0.21784145
## c4_F8R03 0.054202825 0.18574026
## c4_F8R05 0.105438483 0.23194275
## c4_F8R08 0.074848765 0.20202424
## c4_F8R15 0.101135178 0.21686566
## c4_F8R21 0.093903333 0.20298437
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL -0.14072701 0.045250101
## 0_LF_PFOS -0.01992951 0.003989246
## 12_LF_CTRL 0.06875310 -0.053914448
## 12_LF_PFOS 0.07416185 -0.053490211
## 16_LF_CTRL 0.09802162 -0.019799934
## 16_LF_PFOS -0.10607461 -0.016316376
## 21_LF_CTRL 0.11838678 0.089269645
## 21_LF_PFOS -0.01783882 0.018421151
## 8_LF_CTRL 0.05819965 0.005554326
## 8_LF_PFOS 0.03265964 -0.044379029
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 9 0.027001 0.0030001 1.2079 0.3033
## Residuals 74 0.183800 0.0024838## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 1.1237 0.09119 1.9876 0.001 ***
## PFOS 1 0.3040 0.02467 2.1508 0.014 *
## day:PFOS 3 0.2947 0.02392 0.6951 0.966
## Residual 75 10.6003 0.86023
## Total 83 12.3227 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 -0.1941752508 -0.147747095
## c1_F0R06 -0.1553668947 -0.036976864
## c1_F0R07 -0.1950738626 -0.142579804
## c1_F0R08 -0.1511806185 -0.072466009
## c1_F0R09 -0.1602951573 -0.013491619
## c1_F0R12 -0.1572021501 -0.087073671
## c1_F0R14 -0.1650796158 -0.057367605
## c1_F0R15 -0.1681934940 -0.047276177
## c1_F0R24 -0.1563553973 -0.060746585
## c1_F12R09 -0.1532738957 0.043625088
## c1_F12R19 -0.1222666569 0.070353850
## c1_F16R08 -0.1363563679 0.059010216
## c1_F16R20 -0.1414514741 0.023582137
## c1_F16R21 -0.1480488383 0.084982737
## c1_F16R22 -0.1463656993 0.092173360
## c1_F21R19 -0.1285101155 0.102830084
## c1_F21R23 -0.1432627351 0.102702746
## c1_F8R09 -0.1407960327 0.060469930
## c1_F8R12 -0.1667530615 0.010581744
## c1_F8R17 -0.1548535556 0.025393485
## c1_F8R18 -0.1589261399 0.080948104
## c1_F8R22 -0.1845268686 -0.007091743
## c2_F0R01 0.0017616974 -0.091090688
## c2_F0R05 0.0301196984 -0.060861899
## c2_F0R13 0.0069942041 -0.043242370
## c2_F0R17 0.0011058870 -0.101838083
## c2_F0R18 0.0342758387 -0.052129910
## c2_F0R19 0.0062107854 -0.045169380
## c2_F0R20 0.0362892659 -0.032162742
## c2_F12R07 0.0164602773 -0.049316930
## c2_F12R23 0.0378137592 0.019683875
## c2_F16R19 0.0343837919 0.014337718
## c2_F21R10 0.0465070817 0.001157005
## c2_F21R20 0.1027210906 0.003711081
## c2_F21R21 0.0575737885 0.033140721
## c2_F21R24 0.0442085814 0.080610062
## c2_F8R02 0.0552142950 0.016592906
## c2_F8R16 0.0432189521 0.005464639
## c2_F8R20 0.0400845449 -0.024905059
## c3_F0R16 0.0103434147 -0.003237269
## c3_F0R21 0.0283836477 -0.047822636
## c3_F0R23 0.0175415535 -0.012301506
## c3_F12R08 0.0044239548 0.043610581
## c3_F12R10 0.0544173417 0.020840923
## c3_F12R11 0.0161668593 0.061498007
## c3_F12R20 0.0231778369 0.043967289
## c3_F12R21 0.0783288912 0.078824004
## c3_F12R22 0.0546443997 0.086128723
## c3_F16R07 0.0380228573 0.041710601
## c3_F16R11 0.0335952550 0.036592034
## c3_F16R12 0.0423097919 0.051339934
## c3_F16R23 0.0596357226 0.087006987
## c3_F21R09 0.0826958795 0.059300493
## c3_F21R12 0.0204532671 0.046794572
## c3_F21R22 0.0863523664 0.092480792
## c3_F8R04 0.0425510696 0.037919762
## c3_F8R06 0.0102998557 0.086922255
## c3_F8R07 0.0195737496 0.005714659
## c3_F8R10 0.0215608431 -0.030730130
## c3_F8R11 0.0802828052 0.056993089
## c3_F8R13 0.0179295430 0.066766406
## c3_F8R14 0.0174984883 0.058681931
## c3_F8R19 0.0635004953 0.004229776
## c3_F8R23 0.0006981544 0.037038725
## c3_F8R24 0.0269712079 0.067836306
## c4_F0R02 0.0948871437 -0.072655248
## c4_F0R03 0.0534457828 -0.229200095
## c4_F0R10 0.0441682037 -0.132466449
## c4_F0R11 0.0538702657 -0.104038515
## c4_F0R22 0.0917087507 -0.095620122
## c4_F12R12 0.1013091023 0.022575392
## c4_F12R24 0.0973194301 0.009675069
## c4_F16R09 0.1099595686 -0.017030924
## c4_F16R10 0.1099274549 0.022333780
## c4_F16R24 0.1618938443 0.003190014
## c4_F21R07 0.1399269983 0.005974459
## c4_F21R08 0.0975847373 -0.020874829
## c4_F21R11 0.1289734336 -0.006572440
## c4_F8R01 0.0860299083 -0.026781065
## c4_F8R03 0.0623949518 -0.046418165
## c4_F8R05 0.0913782656 -0.029124786
## c4_F8R08 0.0877018234 -0.073316866
## c4_F8R15 0.1548157183 -0.032123933
## c4_F8R21 0.1147157084 -0.013448836
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL -0.064888665 -0.095309815
## 0_LF_PFOS -0.014273138 -0.049736445
## 12_LF_CTRL 0.013410560 0.026633315
## 12_LF_PFOS 0.035659367 0.051140385
## 16_LF_CTRL 0.038606171 0.032794454
## 16_LF_PFOS -0.030618276 0.052129375
## 21_LF_CTRL 0.090080145 0.012614021
## 21_LF_PFOS 0.010013852 0.066274789
## 8_LF_CTRL 0.027130934 0.008219088
## 8_LF_PFOS 0.005474649 0.026659281
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 9 0.014997 0.0016663 1.4086 0.2
## Residuals 74 0.087537 0.0011829## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 0.4791 0.12053 2.7115 0.001 ***
## PFOS 1 0.0917 0.02308 2.0768 0.013 *
## day:PFOS 3 0.0909 0.02287 0.6860 0.953
## Residual 75 3.3132 0.83351
## Total 83 3.9750 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 0.244545916 -0.253028631
## c1_F0R06 -0.257086851 -0.082827091
## c1_F0R07 0.311323474 -0.356169010
## c1_F0R08 -0.283514219 -0.209508809
## c1_F0R09 -0.388486949 -0.107332595
## c1_F0R12 0.109762842 -0.192295004
## c1_F0R14 0.126145678 -0.243832028
## c1_F0R15 0.104891078 -0.136106266
## c1_F0R24 -0.211597215 -0.270888356
## c1_F12R09 0.239532170 -0.084865322
## c1_F12R19 -0.344518287 -0.102651941
## c1_F16R08 0.175067161 -0.080562974
## c1_F16R20 0.024628824 0.016577472
## c1_F16R21 0.223827080 -0.143226047
## c1_F16R22 0.040505482 -0.074193611
## c1_F21R19 -0.277868306 -0.054426186
## c1_F21R23 -0.011750107 -0.023465990
## c1_F8R09 -0.245871896 -0.035657177
## c1_F8R12 0.199485278 -0.224785640
## c1_F8R17 0.185745084 -0.004464066
## c1_F8R18 -0.253067372 -0.052809792
## c1_F8R22 -0.278624022 -0.200739985
## c2_F0R01 0.067965489 -0.143511478
## c2_F0R05 0.164006889 -0.093765638
## c2_F0R13 -0.092281037 -0.014359984
## c2_F0R17 0.174472978 -0.164239061
## c2_F0R18 -0.021529527 -0.163487333
## c2_F0R19 -0.255743310 -0.113327863
## c2_F0R20 -0.191599752 0.016244633
## c2_F12R07 -0.055382101 -0.015757055
## c2_F12R23 0.001100121 0.117490840
## c2_F16R19 -0.276714565 0.067792465
## c2_F21R10 -0.003397936 -0.036252605
## c2_F21R20 0.061827445 0.129455753
## c2_F21R21 0.077489482 0.185735003
## c2_F21R24 -0.183737366 0.085815138
## c2_F8R02 0.014336809 0.076015035
## c2_F8R16 -0.315480105 0.018068344
## c2_F8R20 0.050049662 0.022612119
## c3_F0R16 -0.304786061 -0.007581806
## c3_F0R21 0.230496055 0.122209551
## c3_F0R23 -0.037499529 0.155752092
## c3_F12R08 0.207828798 -0.090026120
## c3_F12R10 -0.053747214 0.121160168
## c3_F12R11 -0.025178539 0.085783414
## c3_F12R20 -0.326041351 0.008156227
## c3_F12R21 0.124767333 0.210006682
## c3_F12R22 0.095935593 0.162081674
## c3_F16R07 0.131087482 -0.025198600
## c3_F16R11 0.127387590 -0.035719130
## c3_F16R12 0.242677664 0.049004975
## c3_F16R23 0.013786416 0.168746824
## c3_F21R09 0.129026946 0.021095780
## c3_F21R12 -0.163112412 0.025788515
## c3_F21R22 -0.011541485 0.189268731
## c3_F8R04 0.152582443 0.178344210
## c3_F8R06 -0.113692151 0.010749508
## c3_F8R07 0.227465084 0.069496769
## c3_F8R10 0.113058502 0.063182811
## c3_F8R11 0.012384066 0.102102791
## c3_F8R13 -0.077397187 0.115935132
## c3_F8R14 -0.169734197 0.100576217
## c3_F8R19 -0.015443075 0.163263938
## c3_F8R23 -0.024946637 0.208493994
## c3_F8R24 -0.127301730 0.028147151
## c4_F0R02 0.049001787 0.123074548
## c4_F0R03 0.157086454 -0.010362501
## c4_F0R10 0.297133676 -0.146568926
## c4_F0R11 -0.090728650 -0.217134937
## c4_F0R22 0.135130180 0.098934472
## c4_F12R12 0.042140924 0.087140099
## c4_F12R24 -0.034227501 0.109382871
## c4_F16R09 -0.022787828 0.106960774
## c4_F16R10 0.141998259 0.114105250
## c4_F16R24 0.163729834 0.155712205
## c4_F21R07 0.226384256 -0.076448947
## c4_F21R08 0.289319016 -0.116290646
## c4_F21R11 0.117444596 0.234288965
## c4_F8R01 -0.349160833 -0.009720934
## c4_F8R03 -0.106938024 0.077648640
## c4_F8R05 0.120785524 0.117693398
## c4_F8R08 -0.104344150 -0.140785361
## c4_F8R15 -0.152415803 0.111074057
## c4_F8R21 0.113927860 0.123206212
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL 0.062781550 -0.142853594
## 0_LF_PFOS -0.033752838 -0.060095849
## 12_LF_CTRL 0.032009012 0.037079140
## 12_LF_PFOS -0.038260207 0.106107451
## 16_LF_CTRL 0.133408710 0.018237825
## 16_LF_PFOS 0.040096053 0.041462739
## 21_LF_CTRL 0.103150651 0.007208962
## 21_LF_PFOS -0.040958535 0.102452419
## 8_LF_CTRL 0.003473225 0.038905651
## 8_LF_PFOS -0.091251184 0.071721063
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 9 0.04865 0.0054052 0.6703 0.733
## Residuals 74 0.59674 0.0080640## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 4 0.7072 0.11482 2.5920 0.002 **
## PFOS 1 0.2456 0.03988 3.6014 0.010 **
## day:PFOS 3 0.0906 0.01470 0.4426 0.960
## Residual 75 5.1157 0.83059
## Total 83 6.1591 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF_no0 bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F12R09 0.333151282 0.021340667
## c1_F12R19 -0.184759531 -0.354848825
## c1_F16R08 0.466905089 -0.167272421
## c1_F16R20 0.143837964 -0.236520012
## c1_F16R21 0.361055747 -0.058793281
## c1_F16R22 0.227666619 -0.126850092
## c1_F21R19 -0.110079172 -0.233878208
## c1_F21R23 0.008091923 -0.018168844
## c1_F8R09 -0.077679770 -0.224312690
## c1_F8R12 0.305763537 -0.109764098
## c1_F8R17 0.108854703 0.111139391
## c1_F8R18 -0.061818761 -0.218542208
## c1_F8R22 0.068927805 -0.410557720
## c2_F12R07 -0.037524990 -0.002160702
## c2_F12R23 -0.135702184 0.157286853
## c2_F16R19 -0.225753400 -0.185075562
## c2_F21R10 -0.048555104 -0.063129979
## c2_F21R20 -0.067768086 0.122831054
## c2_F21R21 -0.014157054 0.132792046
## c2_F21R24 -0.206109344 -0.055618546
## c2_F8R02 -0.009921879 0.031384423
## c2_F8R16 -0.218864145 -0.188694483
## c2_F8R20 0.016621772 0.035446739
## c3_F12R08 0.459389269 -0.056219001
## c3_F12R10 -0.113781629 0.009634377
## c3_F12R11 -0.104205403 -0.039953304
## c3_F12R20 -0.242546533 -0.186696784
## c3_F12R21 -0.049124783 0.269989238
## c3_F12R22 -0.013345965 0.198798576
## c3_F16R07 0.186554892 0.057911545
## c3_F16R11 0.163018283 -0.035489853
## c3_F16R12 0.148344337 0.254457185
## c3_F16R23 -0.167623708 0.167187293
## c3_F21R09 0.078541859 0.065133247
## c3_F21R12 -0.204967750 -0.041282703
## c3_F21R22 -0.150662050 0.159009007
## c3_F8R04 0.002439656 0.175828409
## c3_F8R06 -0.150720271 -0.148520808
## c3_F8R07 0.199422459 0.199901211
## c3_F8R10 0.074552197 0.126442064
## c3_F8R11 -0.147541153 0.100569430
## c3_F8R13 -0.100144079 0.035135797
## c3_F8R14 -0.205153493 -0.097793605
## c3_F8R19 -0.151422375 0.161311824
## c3_F8R23 -0.209571962 0.144474919
## c3_F8R24 -0.049723727 -0.055529326
## c4_F12R12 -0.040399083 0.120184658
## c4_F12R24 -0.154418483 0.073025190
## c4_F16R09 -0.082682325 0.085871774
## c4_F16R10 0.060204587 0.137652053
## c4_F16R24 -0.022527964 0.226141112
## c4_F21R07 0.326570278 0.003425970
## c4_F21R08 0.449547074 -0.021668248
## c4_F21R11 -0.092686235 0.164296969
## c4_F8R01 -0.240614714 -0.261694516
## c4_F8R03 -0.160686353 0.036714874
## c4_F8R05 -0.008939909 0.159743333
## c4_F8R08 0.192490759 -0.218021750
## c4_F8R15 -0.174930540 -0.042484529
## c4_F8R21 0.055161813 0.114480867
##
## $centroids
## PCoA1 PCoA2
## 12_LF_CTRL 0.037300247 0.016222340
## 12_LF_PFOS -0.125702838 0.054564369
## 16_LF_CTRL 0.146863760 0.066846733
## 16_LF_PFOS 0.053531109 -0.025793559
## 21_LF_CTRL 0.092321567 0.019259569
## 21_LF_PFOS -0.096331026 0.019647969
## 8_LF_CTRL -0.005444012 0.005149028
## 8_LF_PFOS -0.086338878 -0.024231963
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.03022 0.0043165 0.5886 0.7621
## Residuals 52 0.38134 0.0073334## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 3 0.6624 0.07200 1.4724 0.052 .
## PFOS 1 0.4148 0.04509 2.7664 0.008 **
## day:PFOS 3 0.3254 0.03537 0.7233 0.874
## Residual 52 7.7973 0.84755
## Total 59 9.1999 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF_no0 jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F12R09 -0.294950423 -0.11061032
## c1_F12R19 -0.299123495 -0.11697759
## c1_F16R08 -0.269748653 -0.11440492
## c1_F16R20 -0.308221402 -0.13201200
## c1_F16R21 -0.305661280 -0.12327398
## c1_F16R22 -0.290463797 -0.09665512
## c1_F21R19 -0.312644375 -0.09819837
## c1_F21R23 -0.300114039 -0.10020415
## c1_F8R09 -0.300739262 -0.09660806
## c1_F8R12 -0.268877810 -0.12804238
## c1_F8R17 -0.275590879 -0.13234066
## c1_F8R18 -0.286441431 -0.07465517
## c1_F8R22 -0.301890262 -0.08341281
## c2_F12R07 -0.012373136 0.05913699
## c2_F12R23 -0.023842929 0.06559290
## c2_F16R19 -0.046982969 0.05998090
## c2_F21R10 -0.029151824 0.12175497
## c2_F21R20 -0.030262061 0.08829049
## c2_F21R21 -0.008548361 0.08504212
## c2_F21R24 -0.016421404 0.10248932
## c2_F8R02 -0.019366439 0.09467155
## c2_F8R16 -0.048535867 0.09512349
## c2_F8R20 -0.028441755 0.05155824
## c3_F12R08 0.145299987 -0.13159236
## c3_F12R10 0.180650334 -0.12094201
## c3_F12R11 0.193992272 -0.09748208
## c3_F12R20 0.148854341 -0.12704453
## c3_F12R21 0.167455767 -0.11616541
## c3_F12R22 0.177679077 -0.11229258
## c3_F16R07 0.186878292 -0.09991175
## c3_F16R11 0.169900230 -0.13011092
## c3_F16R12 0.165911507 -0.10870422
## c3_F16R23 0.173954989 -0.11958070
## c3_F21R09 0.148347842 -0.11176679
## c3_F21R12 0.158758867 -0.14101756
## c3_F21R22 0.185684938 -0.10403829
## c3_F8R04 0.147542953 -0.09826009
## c3_F8R06 0.171399877 -0.11984337
## c3_F8R07 0.163007833 -0.10271571
## c3_F8R10 0.162179945 -0.13285595
## c3_F8R11 0.183741487 -0.10596228
## c3_F8R13 0.170855063 -0.12193546
## c3_F8R14 0.158750757 -0.12694990
## c3_F8R19 0.164739006 -0.12198635
## c3_F8R23 0.133099191 -0.14234124
## c3_F8R24 0.178222202 -0.11488986
## c4_F12R12 0.035978440 0.24481003
## c4_F12R24 0.003044808 0.24037542
## c4_F16R09 0.008847290 0.25356181
## c4_F16R10 0.031646771 0.24965541
## c4_F16R24 0.027672766 0.26258056
## c4_F21R07 0.042290988 0.22258451
## c4_F21R08 0.031698624 0.21209175
## c4_F21R11 0.016722265 0.24030771
## c4_F8R01 -0.024105199 0.21430929
## c4_F8R03 0.002842128 0.19230599
## c4_F8R05 0.029036129 0.27931808
## c4_F8R08 0.002846205 0.21740481
## c4_F8R15 0.015913872 0.22848593
## c4_F8R21 0.017052012 0.23435269
##
## $centroids
## PCoA1 PCoA2
## 12_LF_CTRL 0.06582707 -0.033841705
## 12_LF_PFOS 0.05246790 -0.037945766
## 16_LF_CTRL 0.06576891 0.009887403
## 16_LF_PFOS -0.15844392 -0.040402161
## 21_LF_CTRL 0.05648353 0.108034267
## 21_LF_PFOS -0.07379411 0.009579809
## 8_LF_CTRL 0.03291652 0.020501904
## 8_LF_PFOS 0.01349248 -0.029988707
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.014548 0.0020783 0.6952 0.6757
## Residuals 52 0.155447 0.0029894## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 3 0.4132 0.05039 0.9986 0.464
## PFOS 1 0.3189 0.03890 2.3124 0.009 **
## day:PFOS 3 0.2955 0.03604 0.7143 0.916
## Residual 52 7.1723 0.87467
## Total 59 8.2000 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF_no0 unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F12R09 -0.162926213 0.002135416
## c1_F12R19 -0.154598152 0.055278487
## c1_F16R08 -0.176601761 -0.022281836
## c1_F16R20 -0.168878315 0.061784791
## c1_F16R21 -0.197608478 0.012078123
## c1_F16R22 -0.163677111 0.003736013
## c1_F21R19 -0.163524780 -0.017763191
## c1_F21R23 -0.168115956 0.028154769
## c1_F8R09 -0.150238601 0.033828959
## c1_F8R12 -0.164769291 0.053554130
## c1_F8R17 -0.181984675 -0.050395603
## c1_F8R18 -0.198601576 0.105063734
## c1_F8R22 -0.173594795 0.052374007
## c2_F12R07 0.053043938 0.062108668
## c2_F12R23 0.041185557 -0.017147697
## c2_F16R19 0.012497729 0.022645624
## c2_F21R10 0.042487806 0.092111623
## c2_F21R20 0.023089684 -0.022429413
## c2_F21R21 0.063088232 -0.031869005
## c2_F21R24 0.024904505 0.057611650
## c2_F8R02 0.040015203 -0.024326451
## c2_F8R16 0.009123703 0.070032867
## c2_F8R20 -0.001332093 -0.034928420
## c3_F12R08 -0.013316405 -0.079275383
## c3_F12R10 0.041457678 -0.069062795
## c3_F12R11 0.043257647 -0.082528428
## c3_F12R20 0.013803849 -0.042911843
## c3_F12R21 0.035324426 -0.124426046
## c3_F12R22 0.037160126 -0.037576790
## c3_F16R07 0.049422533 -0.069939244
## c3_F16R11 -0.002003195 -0.006100671
## c3_F16R12 0.044703978 -0.096303907
## c3_F16R23 0.038670899 -0.085214257
## c3_F21R09 0.006014128 -0.102607153
## c3_F21R12 0.028900840 0.004642537
## c3_F21R22 0.041508584 -0.063905784
## c3_F8R04 0.034148673 -0.085163121
## c3_F8R06 -0.001568653 -0.045066187
## c3_F8R07 0.023419452 -0.109949191
## c3_F8R10 0.034352419 -0.087980938
## c3_F8R11 0.037530260 -0.018789757
## c3_F8R13 0.030775589 -0.048783936
## c3_F8R14 0.034845065 -0.084744327
## c3_F8R19 0.052968225 -0.051682498
## c3_F8R23 -0.009188799 -0.051735187
## c3_F8R24 0.006775160 -0.065905005
## c4_F12R12 0.112194230 0.030659495
## c4_F12R24 0.088383766 0.025320777
## c4_F16R09 0.068906775 0.065531050
## c4_F16R10 0.100752620 0.066198956
## c4_F16R24 0.111305523 0.037220341
## c4_F21R07 0.117899966 0.078386765
## c4_F21R08 0.080100473 0.122524062
## c4_F21R11 0.105013941 0.081311240
## c4_F8R01 0.100937345 0.048694540
## c4_F8R03 0.042445224 0.079645058
## c4_F8R05 0.113438845 0.096063713
## c4_F8R08 0.062367119 0.122054644
## c4_F8R15 0.102279588 0.077920782
## c4_F8R21 0.102027545 0.082121242
##
## $centroids
## PCoA1 PCoA2
## 12_LF_CTRL 0.02016465 -0.0300846543
## 12_LF_PFOS 0.01712676 -0.0311575095
## 16_LF_CTRL 0.02356886 -0.0114157800
## 16_LF_PFOS -0.06629149 0.0064367100
## 21_LF_CTRL 0.06855165 0.0542372816
## 21_LF_PFOS -0.01605766 -0.0123017924
## 8_LF_CTRL 0.01985516 0.0004782323
## 8_LF_PFOS -0.00569204 -0.0072139531
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.004116 0.00058798 0.4104 0.8915
## Residuals 52 0.074495 0.00143260## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 3 0.18603 0.07496 1.5366 0.022 *
## PFOS 1 0.09351 0.03768 2.3171 0.012 *
## day:PFOS 3 0.10382 0.04183 0.8575 0.705
## Residual 52 2.09850 0.84554
## Total 59 2.48186 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF_no0 wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F12R09 0.257584927 -1.770580e-01
## c1_F12R19 -0.342736572 -1.364336e-01
## c1_F16R08 0.209480597 -1.871088e-01
## c1_F16R20 0.011176772 -9.293900e-03
## c1_F16R21 0.231173379 -2.002017e-01
## c1_F16R22 0.043974710 -1.366200e-01
## c1_F21R19 -0.267895318 -1.123913e-01
## c1_F21R23 -0.002894491 -8.121009e-02
## c1_F8R09 -0.230561829 -9.974115e-02
## c1_F8R12 0.183846649 -2.181203e-01
## c1_F8R17 0.197755749 -4.775916e-02
## c1_F8R18 -0.238866265 -1.271915e-01
## c1_F8R22 -0.279211821 -2.748954e-01
## c2_F12R07 -0.057705377 -5.437397e-02
## c2_F12R23 0.004007156 7.778114e-02
## c2_F16R19 -0.275933404 4.648430e-02
## c2_F21R10 -0.026074052 5.785979e-03
## c2_F21R20 0.049119962 1.034032e-01
## c2_F21R21 0.079062625 1.541820e-01
## c2_F21R24 -0.170655342 2.107753e-02
## c2_F8R02 0.007531001 7.015701e-02
## c2_F8R16 -0.307111797 -3.175496e-02
## c2_F8R20 0.041794005 2.795365e-05
## c3_F12R08 0.232555314 -1.800636e-01
## c3_F12R10 -0.062214011 1.074136e-01
## c3_F12R11 -0.035855225 8.562905e-02
## c3_F12R20 -0.326389501 -2.387245e-02
## c3_F12R21 0.131265729 1.578622e-01
## c3_F12R22 0.096271718 1.167267e-01
## c3_F16R07 0.132418975 -7.299028e-02
## c3_F16R11 0.120697501 -6.610192e-02
## c3_F16R12 0.253034996 -7.650304e-03
## c3_F16R23 0.013934123 1.342932e-01
## c3_F21R09 0.121689451 1.485884e-02
## c3_F21R12 -0.179038838 1.368739e-02
## c3_F21R22 -0.016546465 1.609773e-01
## c3_F8R04 0.149176094 1.612653e-01
## c3_F8R06 -0.105309822 -3.024280e-02
## c3_F8R07 0.237236441 -3.881360e-03
## c3_F8R10 0.107941490 2.076404e-02
## c3_F8R11 -0.002194584 1.021230e-01
## c3_F8R13 -0.084184555 8.941975e-02
## c3_F8R14 -0.178099207 7.067519e-02
## c3_F8R19 -0.013686119 1.230271e-01
## c3_F8R23 -0.033853532 1.736352e-01
## c3_F8R24 -0.131632714 -6.324330e-03
## c4_F12R12 0.040885579 3.987400e-02
## c4_F12R24 -0.048080737 9.395894e-02
## c4_F16R09 -0.018587891 7.018333e-02
## c4_F16R10 0.141535976 7.567929e-02
## c4_F16R24 0.164342727 1.163992e-01
## c4_F21R07 0.225862411 -1.249688e-01
## c4_F21R08 0.307729595 -1.980950e-01
## c4_F21R11 0.124419893 1.852305e-01
## c4_F8R01 -0.348521833 -4.128643e-02
## c4_F8R03 -0.099699968 2.337786e-02
## c4_F8R05 0.124392197 7.174269e-02
## c4_F8R08 -0.106113298 -2.040260e-01
## c4_F8R15 -0.158604273 8.800444e-02
## c4_F8R21 0.106361098 7.794989e-02
##
## $centroids
## PCoA1 PCoA2
## 12_LF_CTRL 0.032626000 -0.002862647
## 12_LF_PFOS -0.039923926 0.072635448
## 16_LF_CTRL 0.137593534 -0.029970252
## 16_LF_PFOS 0.038494853 0.003309568
## 21_LF_CTRL 0.097841752 -0.011089353
## 21_LF_PFOS -0.040472656 0.061160041
## 8_LF_CTRL 0.002933537 0.005148577
## 8_LF_PFOS -0.094388145 0.035373212
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.02342 0.0033464 0.4456 0.8686
## Residuals 52 0.39047 0.0075090## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 3 0.2295 0.05998 1.2201 0.263
## PFOS 1 0.2456 0.06420 3.9175 0.011 *
## day:PFOS 3 0.0906 0.02367 0.4814 0.954
## Residual 52 3.2607 0.85215
## Total 59 3.8264 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF_d08 bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 0.375062361 0.10161200
## c1_F0R06 -0.125196565 0.28181036
## c1_F0R07 0.512709404 0.14043810
## c1_F0R08 -0.085360835 0.32744870
## c1_F0R09 -0.221910749 0.26355031
## c1_F0R12 0.226069564 0.12585001
## c1_F0R14 0.270202603 0.15587760
## c1_F0R15 0.183044996 0.11489427
## c1_F0R24 0.002241400 0.31727427
## c1_F8R09 -0.168603031 0.15575169
## c1_F8R12 0.288315444 0.04641642
## c1_F8R17 0.150045015 -0.11076730
## c1_F8R18 -0.173462487 0.15133975
## c1_F8R22 -0.086326106 0.25809073
## c2_F0R01 0.160854701 0.04610662
## c2_F0R05 0.218585974 0.04213142
## c2_F0R13 -0.059955858 0.03398444
## c2_F0R17 0.218878915 0.01829742
## c2_F0R18 0.129456732 0.17388925
## c2_F0R19 -0.119307311 0.21444234
## c2_F0R20 -0.137879319 0.10691745
## c2_F8R02 -0.009202910 -0.11308057
## c2_F8R16 -0.285734482 0.11373976
## c2_F8R20 0.049138910 -0.08748247
## c3_F0R16 -0.290691729 0.04639012
## c3_F0R21 0.135056049 -0.28731786
## c3_F0R23 -0.108315733 -0.22483467
## c3_F8R04 -0.005407282 -0.30733351
## c3_F8R06 -0.198853002 0.07166586
## c3_F8R07 0.111305836 -0.28252950
## c3_F8R10 0.069215983 -0.21329306
## c3_F8R11 -0.106099048 -0.16711120
## c3_F8R13 -0.149935129 -0.17250532
## c3_F8R14 -0.272268206 -0.05385977
## c3_F8R19 -0.148186136 -0.26952186
## c3_F8R23 -0.186111780 -0.29738718
## c3_F8R24 -0.128844457 -0.07011691
## c4_F0R02 -0.036947008 -0.20914742
## c4_F0R03 0.158265220 -0.11121415
## c4_F0R10 0.349995163 -0.09093284
## c4_F0R11 0.059375118 0.20093636
## c4_F0R22 0.062343037 -0.17213713
## c4_F8R01 -0.284156943 0.13223757
## c4_F8R03 -0.150097851 -0.11376234
## c4_F8R05 -0.035782540 -0.16403223
## c4_F8R08 0.037511622 0.11871384
## c4_F8R15 -0.222578100 -0.05658976
## c4_F8R21 0.029540553 -0.18484964
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL 0.14759283 0.09114850
## 0_LF_PFOS 0.02270148 0.05359836
## 8_LF_CTRL -0.03521043 -0.08531509
## 8_LF_PFOS -0.12785514 -0.07854599
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.003702 0.0012342 0.1782 0.9106
## Residuals 44 0.304671 0.0069243## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.7005 0.09579 4.8488 0.001 ***
## PFOS 1 0.1112 0.01521 0.7698 0.640
## Residual 45 6.5007 0.88900
## Total 47 7.3123 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF_d08 jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 -0.30599399 -0.05139396
## c1_F0R06 -0.24631939 -0.02062661
## c1_F0R07 -0.31696471 -0.03911493
## c1_F0R08 -0.27322302 -0.01912186
## c1_F0R09 -0.26826260 -0.03784719
## c1_F0R12 -0.29041640 -0.02038200
## c1_F0R14 -0.29811919 -0.02439134
## c1_F0R15 -0.29246173 -0.04350613
## c1_F0R24 -0.27379244 -0.01926907
## c1_F8R09 -0.26775328 -0.03994376
## c1_F8R12 -0.27821168 -0.05311731
## c1_F8R17 -0.24596862 -0.06854332
## c1_F8R18 -0.25279483 -0.02281238
## c1_F8R22 -0.27914931 -0.01776361
## c2_F0R01 0.04990769 0.07632609
## c2_F0R05 0.04826729 0.10354087
## c2_F0R13 0.07668556 0.04990357
## c2_F0R17 0.02643365 0.10373454
## c2_F0R18 0.04094927 0.08907551
## c2_F0R19 0.04320015 0.07183658
## c2_F0R20 0.05001016 0.08940197
## c2_F8R02 0.08426859 0.06624677
## c2_F8R16 0.04713248 0.07793284
## c2_F8R20 0.07111527 0.04584289
## c3_F0R16 0.16771204 -0.18470468
## c3_F0R21 0.17339608 -0.15706421
## c3_F0R23 0.16696054 -0.17876468
## c3_F8R04 0.15211009 -0.17154083
## c3_F8R06 0.15662273 -0.16383028
## c3_F8R07 0.16629766 -0.16512715
## c3_F8R10 0.14039790 -0.14949823
## c3_F8R11 0.18858181 -0.18179532
## c3_F8R13 0.17129279 -0.21463946
## c3_F8R14 0.16601990 -0.20160829
## c3_F8R19 0.18718481 -0.20310474
## c3_F8R23 0.14357408 -0.22230196
## c3_F8R24 0.19040087 -0.18367730
## c4_F0R02 0.11365764 0.18599343
## c4_F0R03 0.04687180 0.16096087
## c4_F0R10 0.06977495 0.21465851
## c4_F0R11 0.10884483 0.21100848
## c4_F0R22 0.11743860 0.19724808
## c4_F8R01 0.09698453 0.18002461
## c4_F8R03 0.09406166 0.15760521
## c4_F8R05 0.14457079 0.20617120
## c4_F8R08 0.11701149 0.19977992
## c4_F8R15 0.12702658 0.15778530
## c4_F8R21 0.14466689 0.21041332
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL -0.118511930 0.05673530
## 0_LF_PFOS 0.006954404 0.01038449
## 8_LF_CTRL 0.079719419 -0.01235227
## 8_LF_PFOS 0.055824937 -0.06177142
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.004685 0.0015616 0.8037 0.4986
## Residuals 44 0.085493 0.0019430## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.4411 0.06188 3.0177 0.001 ***
## PFOS 1 0.1097 0.01539 0.7505 0.761
## Residual 45 6.5780 0.92273
## Total 47 7.1288 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF_d08 unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 -0.185991383 -0.141563823
## c1_F0R06 -0.152944014 0.030071303
## c1_F0R07 -0.191971397 -0.058812271
## c1_F0R08 -0.143144547 0.044271105
## c1_F0R09 -0.146969243 0.045814098
## c1_F0R12 -0.153137092 -0.054477889
## c1_F0R14 -0.147825383 -0.078938105
## c1_F0R15 -0.163314325 -0.012669408
## c1_F0R24 -0.156723120 0.037803413
## c1_F8R09 -0.126330858 0.055781651
## c1_F8R12 -0.145780561 -0.007195726
## c1_F8R17 -0.142084311 0.051877278
## c1_F8R18 -0.121170821 0.109519665
## c1_F8R22 -0.136446564 0.073935333
## c2_F0R01 0.049954532 -0.002039293
## c2_F0R05 0.043543300 -0.052289778
## c2_F0R13 0.030320882 -0.063479534
## c2_F0R17 0.033883080 -0.051718129
## c2_F0R18 0.035088092 -0.031239198
## c2_F0R19 0.025082759 -0.045559741
## c2_F0R20 0.065063284 -0.055492323
## c2_F8R02 0.067535465 0.075613386
## c2_F8R16 0.043955852 0.015008159
## c2_F8R20 0.039729777 0.002025649
## c3_F0R16 0.050524557 0.038954800
## c3_F0R21 0.068764456 0.039320416
## c3_F0R23 0.029675374 0.020120616
## c3_F8R04 0.055096431 0.038981654
## c3_F8R06 0.044841766 0.066681761
## c3_F8R07 0.054672474 0.056597836
## c3_F8R10 0.027622109 0.054032760
## c3_F8R11 0.088198710 0.078581922
## c3_F8R13 0.074886193 0.096428492
## c3_F8R14 0.062806539 0.039309823
## c3_F8R19 0.075677575 0.043118778
## c3_F8R23 0.015837480 0.090184574
## c3_F8R24 0.046275396 0.110379567
## c4_F0R02 0.110949080 -0.066665236
## c4_F0R03 0.009233309 -0.224064680
## c4_F0R10 0.046664554 -0.117614500
## c4_F0R11 0.072204119 -0.085277922
## c4_F0R22 0.088115497 -0.064644216
## c4_F8R01 0.121888650 0.062165263
## c4_F8R03 0.045168674 -0.050046131
## c4_F8R05 0.103248392 -0.049143585
## c4_F8R08 0.129625661 -0.033257695
## c4_F8R15 0.131373870 -0.003852683
## c4_F8R21 0.126325733 -0.026537432
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL -0.057039301 -0.05038022
## 0_LF_PFOS 0.006503744 -0.02594705
## 8_LF_CTRL 0.043416427 0.03399329
## 8_LF_PFOS 0.024264711 0.05243104
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.009440 0.0031467 2.4418 0.0768 .
## Residuals 44 0.056702 0.0012887
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.18544 0.08204 4.0968 0.001 ***
## PFOS 1 0.03812 0.01686 0.8421 0.644
## Residual 45 2.03690 0.90110
## Total 47 2.26046 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF_d08 wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 0.287854628 -0.207470593
## c1_F0R06 -0.251289090 -0.068594135
## c1_F0R07 0.359994236 -0.302385928
## c1_F0R08 -0.245433374 -0.184194065
## c1_F0R09 -0.361366164 -0.105171986
## c1_F0R12 0.162593310 -0.162998412
## c1_F0R14 0.176393465 -0.213775031
## c1_F0R15 0.133220331 -0.102586115
## c1_F0R24 -0.152966264 -0.260019218
## c1_F8R09 -0.240762573 -0.019934564
## c1_F8R12 0.230678015 -0.169335795
## c1_F8R17 0.190005183 0.042674307
## c1_F8R18 -0.248395318 -0.032862068
## c1_F8R22 -0.255234727 -0.156060441
## c2_F0R01 0.121610641 -0.117641505
## c2_F0R05 0.185072000 -0.063450635
## c2_F0R13 -0.067251711 0.011018792
## c2_F0R17 0.233201183 -0.139234548
## c2_F0R18 0.016671169 -0.126607765
## c2_F0R19 -0.234158191 -0.089018736
## c2_F0R20 -0.165601198 0.028486600
## c2_F8R02 0.038285898 0.108712738
## c2_F8R16 -0.300821320 0.019664804
## c2_F8R20 0.071344372 0.059043447
## c3_F0R16 -0.299756607 -0.004464084
## c3_F0R21 0.221072723 0.192438337
## c3_F0R23 -0.015923384 0.181505868
## c3_F8R04 0.161653030 0.233584872
## c3_F8R06 -0.103232587 0.028985499
## c3_F8R07 0.212018911 0.136090748
## c3_F8R10 0.122884182 0.110057025
## c3_F8R11 0.040209404 0.123677076
## c3_F8R13 -0.060396766 0.140417536
## c3_F8R14 -0.151770845 0.119193564
## c3_F8R19 -0.005075499 0.190980124
## c3_F8R23 -0.008205271 0.238527895
## c3_F8R24 -0.108485997 0.057682358
## c4_F0R02 0.067985939 0.157989526
## c4_F0R03 0.200615793 0.028286432
## c4_F0R10 0.333265861 -0.086338194
## c4_F0R11 -0.041703624 -0.190487074
## c4_F0R22 0.145888054 0.137842070
## c4_F8R01 -0.320971574 -0.007814685
## c4_F8R03 -0.100763383 0.099867244
## c4_F8R05 0.126181305 0.156306954
## c4_F8R08 -0.089446543 -0.088086546
## c4_F8R15 -0.132335899 0.126139431
## c4_F8R21 0.122648278 0.169358877
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL 0.103585190 -0.11098382
## 0_LF_PFOS -0.005619242 -0.03343873
## 8_LF_CTRL 0.017433299 0.07401032
## 8_LF_PFOS -0.077811612 0.09745743
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.01737 0.0057890 0.6793 0.5694
## Residuals 44 0.37499 0.0085224## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.3452 0.09478 4.7885 0.004 **
## PFOS 1 0.0530 0.01455 0.7352 0.510
## Residual 45 3.2440 0.89067
## Total 47 3.6421 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF-CTRL_d08 bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 0.33808035 0.137815355
## c1_F0R30 -0.20051652 0.024158141
## c1_F0R33 0.19353730 -0.037168338
## c1_F0R35 -0.15938095 0.201751499
## c1_F0R36 -0.26433409 0.111840505
## c1_F8R29 -0.21127020 0.090493428
## c1_F8R34 -0.13138436 0.103270503
## c1_F8R36 -0.03179466 0.060225467
## c2_F0R25 -0.02679280 0.013217016
## c2_F0R29 -0.20101278 -0.105483294
## c2_F0R34 -0.16591611 0.037013087
## c2_F8R31 -0.24072187 0.112432628
## c2_F8R35 -0.24260737 0.126850435
## c3_F0R26 -0.08226937 -0.226566586
## c3_F8R26 -0.13389207 -0.068126321
## c3_F8R27 0.14081987 -0.225536099
## c3_F8R32 0.45247604 0.051049177
## c4_F0R27 -0.09909073 -0.186153397
## c4_F0R31 -0.10437488 -0.082749180
## c4_F0R32 -0.08988430 0.109692154
## c4_F8R25 0.19799590 -0.052750287
## c4_F8R28 0.56969208 0.212815660
## c4_F8R30 0.10265840 -0.406951809
## c4_F8R33 0.38998312 -0.001139746
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL -0.112708161 0.001273696
## 8_HF_CTRL -0.002384038 0.010739859
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.07115 0.071152 3.9253 0.0602 .
## Residuals 22 0.39878 0.018127
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.21974 0.071 1.6814 0.121
## Residual 22 2.87516 0.929
## Total 23 3.09490 1.000
## [1] ""
## [1] "Processing Feces_HF-CTRL_d08 jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 -0.21117479 -0.226541687
## c1_F0R30 -0.29287819 0.008047630
## c1_F0R33 -0.24815617 -0.173505865
## c1_F0R35 -0.22982968 -0.185535252
## c1_F0R36 -0.28208831 0.093254521
## c1_F8R29 -0.26288075 0.029395400
## c1_F8R34 -0.26499871 -0.047614312
## c1_F8R36 -0.27369665 0.003052878
## c2_F0R25 0.11024596 -0.160835520
## c2_F0R29 0.07145232 0.175668069
## c2_F0R34 0.06619174 0.087177501
## c2_F8R31 0.06075467 0.144018277
## c2_F8R35 0.01373991 0.206486444
## c3_F0R26 0.04487053 0.277780698
## c3_F8R26 0.04556541 0.231420983
## c3_F8R27 0.09287467 0.204139012
## c3_F8R32 0.13096854 0.018124082
## c4_F0R27 0.16921529 0.039848254
## c4_F0R31 0.17785517 0.066934447
## c4_F0R32 0.22989203 -0.120178303
## c4_F8R25 0.22699859 -0.224567077
## c4_F8R28 0.25129030 -0.254518233
## c4_F8R30 0.16675145 0.044004840
## c4_F8R33 0.20703667 -0.236056787
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL -0.03242921 -0.009322845
## 8_HF_CTRL 0.03005433 0.011794570
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.0000901 0.00009006 0.1759 0.679
## Residuals 22 0.0112650 0.00051205## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.1638 0.04361 1.0031 0.384
## Residual 22 3.5917 0.95639
## Total 23 3.7555 1.00000
## [1] ""
## [1] "Processing Feces_HF-CTRL_d08 unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 -0.09765545 -0.18205999
## c1_F0R30 0.09359695 -0.14668797
## c1_F0R33 -0.05444863 -0.16499813
## c1_F0R35 -0.08164593 -0.18996974
## c1_F0R36 0.16107977 -0.07627914
## c1_F8R29 0.06245185 -0.12014402
## c1_F8R34 0.07956032 -0.13918523
## c1_F8R36 0.09182365 -0.09084155
## c2_F0R25 -0.16928016 -0.02190610
## c2_F0R29 0.07790414 0.09761467
## c2_F0R34 0.02954121 0.03800644
## c2_F8R31 0.09747415 0.04766546
## c2_F8R35 0.16078913 0.04712993
## c3_F0R26 0.14234662 0.06045129
## c3_F8R26 0.11213190 0.09207697
## c3_F8R27 0.06559485 0.10982376
## c3_F8R32 -0.07003304 0.03486856
## c4_F0R27 0.02189133 0.12667652
## c4_F0R31 0.06747962 0.13408006
## c4_F0R32 -0.10311586 0.06228994
## c4_F8R25 -0.23990314 0.08588417
## c4_F8R28 -0.22458566 0.06128768
## c4_F8R30 -0.02106182 0.10163780
## c4_F8R33 -0.20193581 0.03257864
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL 0.012866937 -0.02014633
## 8_HF_CTRL 0.003627713 0.01830543
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.0000096 0.00000965 0.0128 0.9109
## Residuals 22 0.0165604 0.00075274## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.05639 0.04391 1.0105 0.38
## Residual 22 1.22771 0.95609
## Total 23 1.28410 1.00000
## [1] ""
## [1] "Processing Feces_HF-CTRL_d08 wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R28 -0.0735028840 0.22416998
## c1_F0R30 0.1310774180 -0.06871826
## c1_F0R33 -0.2453923367 0.05576272
## c1_F0R35 0.2149532811 0.15129617
## c1_F0R36 0.2698750017 -0.01533305
## c1_F8R29 0.2037981455 -0.03476637
## c1_F8R34 0.1822425567 -0.01510408
## c1_F8R36 0.0343003363 -0.02885767
## c2_F0R25 0.0361111293 -0.03572085
## c2_F0R29 0.0495192790 -0.11759238
## c2_F0R34 0.1612946545 -0.01886938
## c2_F8R31 0.2741321105 0.02473122
## c2_F8R35 0.3002060712 0.04402388
## c3_F0R26 -0.1279469083 -0.13076542
## c3_F8R26 0.0592099795 -0.05325323
## c3_F8R27 -0.1691131753 0.02277040
## c3_F8R32 -0.2360850348 0.11803929
## c4_F0R27 -0.0587461404 -0.07771509
## c4_F0R31 -0.0002456854 -0.03647138
## c4_F0R32 0.1204039906 0.04242380
## c4_F8R25 -0.2076453393 0.03289022
## c4_F8R28 -0.3208284932 0.09655696
## c4_F8R30 -0.3160431276 -0.21749375
## c4_F8R33 -0.2815748290 0.03799625
##
## $centroids
## PCoA1 PCoA2
## 0_HF_CTRL 0.06077410 -0.019120754
## 8_HF_CTRL -0.01858918 -0.001712886
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.035519 0.035519 4.3499 0.04882 *
## Residuals 22 0.179639 0.008165
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.06849 0.04342 0.9985 0.365
## Residual 22 1.50906 0.95658
## Total 23 1.57755 1.00000
## [1] ""
## [1] "Processing Feces_LF-CTRL_d08 bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 0.283402310 -0.1964202907
## c1_F0R06 -0.261418751 -0.2019636867
## c1_F0R07 0.413397551 -0.2495202735
## c1_F0R08 -0.211905628 -0.2675604856
## c1_F0R09 -0.331139740 -0.1995783305
## c1_F0R12 0.126994398 -0.1907641396
## c1_F8R09 -0.245068842 -0.0738037766
## c1_F8R12 0.237911632 -0.1218551886
## c2_F0R01 0.100257370 -0.0684837609
## c2_F0R05 0.160140096 -0.0370813013
## c2_F8R02 -0.036947988 0.1392979602
## c3_F8R04 0.011512323 0.3005249165
## c3_F8R06 -0.266014306 -0.0003094766
## c3_F8R07 0.182129821 0.2536712656
## c3_F8R10 0.089619933 0.2182703916
## c3_F8R11 -0.088079917 0.1970840709
## c4_F0R02 -0.036480088 0.2485373601
## c4_F0R03 0.133331575 0.1019493339
## c4_F0R10 0.329639473 0.0256529329
## c4_F0R11 -0.019143443 -0.1827289090
## c4_F8R01 -0.348328853 -0.0293269692
## c4_F8R03 -0.167179145 0.1888006258
## c4_F8R05 -0.048788229 0.2349742817
## c4_F8R08 -0.007841552 -0.0893665506
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL 0.07577470 -0.1049157
## 8_LF_CTRL -0.05030367 0.1171862
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.000265 0.0002646 0.0343 0.8548
## Residuals 22 0.169805 0.0077184## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.4128 0.11041 2.7306 0.007 **
## Residual 22 3.3259 0.88959
## Total 23 3.7387 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF-CTRL_d08 jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 -0.30303748 -0.065711120
## c1_F0R06 -0.23857828 0.021533588
## c1_F0R07 -0.32127960 -0.080302559
## c1_F0R08 -0.27038694 -0.015308869
## c1_F0R09 -0.26747741 0.017763474
## c1_F0R12 -0.27891728 -0.040097301
## c1_F8R09 -0.26073568 0.026085605
## c1_F8R12 -0.27604347 0.017980500
## c2_F0R01 0.04882264 0.004401737
## c2_F0R05 0.07161830 -0.036625802
## c2_F8R02 0.08755359 0.012324181
## c3_F8R04 0.12461984 0.225910229
## c3_F8R06 0.11578303 0.272906918
## c3_F8R07 0.12654012 0.267376391
## c3_F8R10 0.09811669 0.225256273
## c3_F8R11 0.13928329 0.273757716
## c4_F0R02 0.15844238 -0.149740638
## c4_F0R03 0.15473441 -0.170264347
## c4_F0R10 0.14412595 -0.229963450
## c4_F0R11 0.20318092 -0.134275057
## c4_F8R01 0.16391294 -0.127511636
## c4_F8R03 0.18059016 -0.099858298
## c4_F8R05 0.22565837 -0.096395898
## c4_F8R08 0.17347352 -0.119241637
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL -0.09222768 -0.06757483
## 8_LF_CTRL 0.08841478 0.07763743
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.003627 0.0036270 1.9112 0.1807
## Residuals 22 0.041751 0.0018978## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.3497 0.09443 2.294 0.021 *
## Residual 22 3.3540 0.90557
## Total 23 3.7038 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF-CTRL_d08 unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 -0.16961876 0.0696653594
## c1_F0R06 -0.15829553 0.0231140500
## c1_F0R07 -0.19005020 0.1251085144
## c1_F0R08 -0.13422099 0.0394611853
## c1_F0R09 -0.16656353 -0.0398813887
## c1_F0R12 -0.13173622 0.0230403886
## c1_F8R09 -0.15219859 -0.0855053065
## c1_F8R12 -0.14895057 -0.0585670544
## c2_F0R01 0.01914881 0.0609791585
## c2_F0R05 0.05836911 0.0802964954
## c2_F8R02 0.04964497 0.0062263545
## c3_F8R04 0.05043814 -0.1183176112
## c3_F8R06 0.03238363 -0.1643864049
## c3_F8R07 0.02212894 -0.1345097627
## c3_F8R10 0.03269284 -0.1042417477
## c3_F8R11 0.08160942 -0.0930014963
## c4_F0R02 0.11275917 0.0551888074
## c4_F0R03 0.12689154 0.1113194592
## c4_F0R10 0.07277985 0.1434295081
## c4_F0R11 0.11518789 0.0866394894
## c4_F8R01 0.11952981 -0.0006962253
## c4_F8R03 0.10640632 -0.0401456977
## c4_F8R05 0.12529252 -0.0234684158
## c4_F8R08 0.12637142 0.0382523410
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL -0.04270756 0.06219204
## 8_LF_CTRL 0.04553247 -0.06794702
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.0037608 0.0037608 3.1709 0.08878 .
## Residuals 22 0.0260926 0.0011860
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.14265 0.11708 2.9172 0.002 **
## Residual 22 1.07576 0.88292
## Total 23 1.21840 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF-CTRL_d08 wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R04 0.250722210 -0.173109604
## c1_F0R06 -0.287059678 -0.040343829
## c1_F0R07 0.332281413 -0.253347129
## c1_F0R08 -0.275606537 -0.171295467
## c1_F0R09 -0.393171871 -0.116579060
## c1_F0R12 0.128099893 -0.141600594
## c1_F8R09 -0.282847485 -0.012767039
## c1_F8R12 0.200272974 -0.143179433
## c2_F0R01 0.091123324 -0.099333492
## c2_F0R05 0.147756751 -0.020167836
## c2_F8R02 -0.010379576 0.131275889
## c3_F8R04 0.113453895 0.245870004
## c3_F8R06 -0.150369796 0.054676453
## c3_F8R07 0.181914522 0.164093440
## c3_F8R10 0.083176311 0.146083057
## c3_F8R11 -0.005884765 0.139838514
## c4_F0R02 0.016961986 0.188604410
## c4_F0R03 0.162744892 0.064662803
## c4_F0R10 0.304523968 -0.036575673
## c4_F0R11 -0.062345322 -0.176042115
## c4_F8R01 -0.357647765 -0.002099581
## c4_F8R03 -0.150927837 0.128547996
## c4_F8R05 0.077955972 0.196589629
## c4_F8R08 -0.114747478 -0.073801340
##
## $centroids
## PCoA1 PCoA2
## 0_LF_CTRL 0.07359920 -0.08428073
## 8_LF_CTRL -0.02547525 0.09764896
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.003355 0.0033554 0.3251 0.5744
## Residuals 22 0.227089 0.0103222## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.20517 0.10519 2.5863 0.051 .
## Residual 22 1.74520 0.89481
## Total 23 1.95036 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF-PFOS_d08 bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R38 -0.15919179 0.169290528
## c1_F0R40 0.08426738 0.074142404
## c1_F0R42 -0.36891673 0.058778171
## c1_F0R44 -0.10087341 -0.024355147
## c1_F0R45 -0.35333120 0.046137420
## c1_F0R47 -0.27655239 0.095833206
## c1_F8R39 0.16878789 -0.053855024
## c1_F8R40 -0.19325820 0.112669329
## c1_F8R46 -0.29558231 -0.028548696
## c1_F8R48 -0.13891204 -0.071196735
## c2_F0R37 0.05560542 0.117007660
## c2_F0R39 -0.03588524 0.009908223
## c2_F0R43 -0.15868821 0.147029855
## c2_F0R48 -0.04878600 -0.316954464
## c2_F8R41 -0.08771188 0.006111541
## c2_F8R42 0.14550910 -0.442682839
## c2_F8R43 0.45907724 0.168431438
## c2_F8R44 0.47670284 0.164013781
## c2_F8R47 0.25743231 -0.039592288
## c3_F0R41 -0.36331233 0.015213589
## c3_F8R38 0.48290680 -0.021854422
## c3_F8R45 0.29633883 -0.162086074
## c4_F0R46 -0.34489056 -0.109504507
## c4_F8R37 0.49926448 0.086063049
##
## $centroids
## PCoA1 PCoA2
## 0_HF_PFOS -0.2013605 0.04190523
## 8_HF_PFOS 0.1718758 -0.02091117
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.10748 0.107482 13.841 0.00119 **
## Residuals 22 0.17084 0.007765
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.8231 0.21032 5.8594 0.004 **
## Residual 22 3.0905 0.78968
## Total 23 3.9136 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF-PFOS_d08 jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R38 -0.14373906 -0.21339877
## c1_F0R40 -0.08965223 -0.26616384
## c1_F0R42 -0.32389091 0.07303711
## c1_F0R44 -0.26831958 0.01431509
## c1_F0R45 -0.31743886 0.05530464
## c1_F0R47 -0.10297307 -0.24332845
## c1_F8R39 -0.11894532 -0.18405712
## c1_F8R40 -0.10805066 -0.25149393
## c1_F8R46 -0.31132828 0.04955494
## c1_F8R48 -0.24620344 -0.02288686
## c2_F0R37 0.19306852 0.01775830
## c2_F0R39 0.19067934 0.03750879
## c2_F0R43 0.22005009 -0.07632999
## c2_F0R48 0.06212072 0.27979675
## c2_F8R41 0.11868464 0.08189546
## c2_F8R42 0.05668937 0.20020181
## c2_F8R43 0.24755151 -0.11713348
## c2_F8R44 0.29116355 -0.12330245
## c2_F8R47 0.23618116 -0.02638201
## c3_F0R41 -0.10683609 0.29396872
## c3_F8R38 0.20177829 0.06664946
## c3_F8R45 0.16445309 0.09707876
## c4_F0R46 -0.09570465 0.28134327
## c4_F8R37 0.25066185 -0.02393621
##
## $centroids
## PCoA1 PCoA2
## 0_HF_PFOS -0.07446725 0.01240365
## 8_HF_PFOS 0.08011498 -0.02354291
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.000821 0.00082084 0.4343 0.5167
## Residuals 22 0.041576 0.00188981## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.2928 0.07549 1.7965 0.056 .
## Residual 22 3.5851 0.92451
## Total 23 3.8779 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF-PFOS_d08 unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R38 -0.045156669 -0.152334459
## c1_F0R40 0.032908348 -0.146840399
## c1_F0R42 -0.213979606 -0.018295560
## c1_F0R44 -0.187680324 -0.014250136
## c1_F0R45 -0.167483911 -0.015971933
## c1_F0R47 0.005741474 -0.172195113
## c1_F8R39 -0.052842650 -0.100682177
## c1_F8R40 -0.065868509 -0.125889921
## c1_F8R46 -0.166083146 -0.019568696
## c1_F8R48 -0.152507194 -0.032941034
## c2_F0R37 0.150670243 0.040712540
## c2_F0R39 0.058471137 0.062927058
## c2_F0R43 0.153413479 -0.069060576
## c2_F0R48 -0.030766055 0.234543144
## c2_F8R41 0.052525008 0.052564227
## c2_F8R42 -0.040513853 0.119332024
## c2_F8R43 0.161665713 -0.040671678
## c2_F8R44 0.182826187 -0.030605962
## c2_F8R47 0.132573504 0.002092434
## c3_F0R41 -0.152779152 0.137980598
## c3_F8R38 0.120556099 0.039153240
## c3_F8R45 0.125358976 0.073038222
## c4_F0R46 -0.103775705 0.126965877
## c4_F8R37 0.202726605 0.049998283
##
## $centroids
## PCoA1 PCoA2
## 0_HF_PFOS -0.04724032 -0.0088684780
## 8_HF_PFOS 0.05334838 0.0002989261
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.0051588 0.0051588 4.6356 0.04254 *
## Residuals 22 0.0244833 0.0011129
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.11791 0.08508 2.0459 0.028 *
## Residual 22 1.26794 0.91492
## Total 23 1.38585 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_HF-PFOS_d08 wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R38 0.18793517 -0.13331820
## c1_F0R40 -0.03726618 -0.17080713
## c1_F0R42 0.34525708 0.02163683
## c1_F0R44 -0.05162170 -0.05083180
## c1_F0R45 0.32644329 0.03183851
## c1_F0R47 0.20338888 0.01136758
## c1_F8R39 -0.18789149 -0.08575228
## c1_F8R40 0.22511769 -0.03684472
## c1_F8R46 0.24278639 0.07947552
## c1_F8R48 0.06260781 0.02670948
## c2_F0R37 -0.07342456 -0.14971369
## c2_F0R39 -0.01110032 -0.05247531
## c2_F0R43 0.19781936 -0.01475746
## c2_F0R48 -0.17607680 0.19645087
## c2_F8R41 0.08582040 0.06924044
## c2_F8R42 -0.27247164 0.29548590
## c2_F8R43 -0.08448338 -0.13028510
## c2_F8R44 -0.12872947 -0.13013120
## c2_F8R47 -0.16698902 -0.04434079
## c3_F0R41 0.24272465 0.08587508
## c3_F8R38 -0.44877685 -0.04775065
## c3_F8R45 -0.28709197 0.13343778
## c4_F0R46 0.22348383 0.10663063
## c4_F8R37 -0.41746116 -0.01114031
##
## $centroids
## PCoA1 PCoA2
## 0_HF_PFOS 0.1638529 3.786924e-05
## 8_HF_PFOS -0.1144473 -1.114095e-02
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.031436 0.0314356 3.2928 0.08324 .
## Residuals 22 0.210028 0.0095467
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.35023 0.17885 4.7916 0.013 *
## Residual 22 1.60806 0.82115
## Total 23 1.95829 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF-PFOS_d08 bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R14 -0.269614498 -0.246030025
## c1_F0R15 -0.185372163 -0.206216060
## c1_F0R24 -0.328891943 0.087723586
## c1_F8R17 -0.032196590 -0.263646236
## c1_F8R18 -0.119168210 0.187199797
## c1_F8R22 -0.240777061 0.205571327
## c2_F0R13 -0.044395472 -0.002575737
## c2_F0R17 -0.088385929 -0.259111858
## c2_F0R18 -0.243819684 -0.049961688
## c2_F0R19 -0.190972636 0.164115613
## c2_F0R20 -0.088000640 0.074280205
## c2_F8R16 -0.026523850 0.263881431
## c2_F8R20 0.002078455 -0.116471745
## c3_F0R16 0.051996063 0.247100009
## c3_F0R21 0.206400184 -0.205748136
## c3_F0R23 0.232526876 -0.057156766
## c3_F8R13 0.201135421 0.037713271
## c3_F8R14 0.142273345 0.214501825
## c3_F8R19 0.273933768 0.010431003
## c3_F8R23 0.324228872 0.038078146
## c3_F8R24 0.094911049 0.102420472
## c4_F0R22 0.097915368 -0.193507729
## c4_F8R15 0.115758361 0.131692935
## c4_F8R21 0.114960914 -0.164283639
##
## $centroids
## PCoA1 PCoA2
## 0_LF_PFOS -0.08468957 -0.05027336
## 8_LF_PFOS 0.09048932 0.05978177
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.000001 0.0000012 2e-04 0.9889
## Residuals 22 0.138275 0.0062852## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.3480 0.10376 2.5471 0.006 **
## Residual 22 3.0055 0.89624
## Total 23 3.3535 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF-PFOS_d08 jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R14 -0.297296407 -0.10554923
## c1_F0R15 -0.302631248 -0.11555271
## c1_F0R24 -0.307902551 -0.08297052
## c1_F8R17 -0.286556055 -0.14298622
## c1_F8R18 -0.285883457 -0.08552973
## c1_F8R22 -0.302070088 -0.10798115
## c2_F0R13 0.002184925 0.17243410
## c2_F0R17 -0.032969563 0.18529307
## c2_F0R18 -0.010553614 0.18599705
## c2_F0R19 0.013876339 0.18610823
## c2_F0R20 0.013901101 0.19164220
## c2_F8R16 0.020081428 0.16658670
## c2_F8R20 0.030380822 0.16621464
## c3_F0R16 0.201887421 -0.14403650
## c3_F0R21 0.197417871 -0.10021624
## c3_F0R23 0.196547155 -0.13358703
## c3_F8R13 0.208520560 -0.13368215
## c3_F8R14 0.177422192 -0.17448672
## c3_F8R19 0.235096419 -0.12562044
## c3_F8R23 0.177143141 -0.16823317
## c3_F8R24 0.212574949 -0.11840278
## c4_F0R22 0.034582285 0.15400876
## c4_F8R15 0.051505050 0.15226449
## c4_F8R21 0.052741326 0.17828534
##
## $centroids
## PCoA1 PCoA2
## 0_LF_PFOS -0.01662251 0.05291427
## 8_LF_PFOS 0.05044912 -0.03527128
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.000035 0.00003476 0.0115 0.9156
## Residuals 22 0.066487 0.00302213## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.19397 0.06491 1.5271 0.114
## Residual 22 2.79440 0.93509
## Total 23 2.98837 1.00000
## [1] ""
## [1] "Processing Feces_LF-PFOS_d08 unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R14 0.16639285 0.071907032
## c1_F0R15 0.15595046 0.057244866
## c1_F0R24 0.16353114 0.020993723
## c1_F8R17 0.19633403 -0.037643299
## c1_F8R18 0.15834375 -0.065938553
## c1_F8R22 0.17571004 -0.105764019
## c2_F0R13 -0.03938303 0.057089553
## c2_F0R17 -0.01443805 0.126307319
## c2_F0R18 -0.02490914 0.100454952
## c2_F0R19 -0.02437868 0.081942922
## c2_F0R20 -0.03687267 0.109621263
## c2_F8R16 -0.03239643 -0.015251583
## c2_F8R20 -0.06337281 -0.004445988
## c3_F0R16 -0.07254928 -0.037420447
## c3_F0R21 -0.07914061 -0.013409442
## c3_F0R23 -0.03896573 0.040739709
## c3_F8R13 -0.06161656 -0.089710455
## c3_F8R14 -0.04132681 -0.057354016
## c3_F8R19 -0.09107419 -0.046695293
## c3_F8R23 -0.02174382 -0.086938939
## c3_F8R24 -0.06729415 -0.095200216
## c4_F0R22 -0.09092457 0.019967738
## c4_F8R15 -0.11314588 0.002423506
## c4_F8R21 -0.10272986 -0.032920335
##
## $centroids
## PCoA1 PCoA2
## 0_LF_PFOS -0.004031542 0.05837185
## 8_LF_PFOS -0.022068330 -0.05410601
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.000015 0.00001537 0.0093 0.9241
## Residuals 22 0.036406 0.00165481## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.08655 0.10264 2.5164 0.018 *
## Residual 22 0.75664 0.89736
## Total 23 0.84318 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Feces_LF-PFOS_d08 wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_F0R14 0.144161160 -0.288031253
## c1_F0R15 0.140402395 -0.172323277
## c1_F0R24 -0.202422984 -0.240367531
## c1_F8R17 0.225959211 -0.081056509
## c1_F8R18 -0.218052010 0.007620927
## c1_F8R22 -0.283889253 -0.091196851
## c2_F0R13 -0.023573001 -0.011539102
## c2_F0R17 0.217039993 -0.227047919
## c2_F0R18 0.001867268 -0.153371979
## c2_F0R19 -0.226568102 -0.055894307
## c2_F0R20 -0.118922722 0.031697852
## c2_F8R16 -0.252404271 0.070043223
## c2_F8R20 0.112395166 -0.007311836
## c3_F0R16 -0.248822338 0.040725888
## c3_F0R21 0.277616846 0.108629113
## c3_F0R23 0.078093449 0.138397757
## c3_F8R13 0.012965492 0.117600136
## c3_F8R14 -0.082646848 0.129043876
## c3_F8R19 0.082571130 0.144132823
## c3_F8R23 0.091138279 0.199218496
## c3_F8R24 -0.067866764 0.057989305
## c4_F0R22 0.211555883 0.054913264
## c4_F8R15 -0.060532467 0.130601814
## c4_F8R21 0.189934488 0.097526092
##
## $centroids
## PCoA1 PCoA2
## 0_LF_PFOS 0.01508737 -0.06456554
## 8_LF_PFOS -0.01914584 0.08294060
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.007286 0.0072856 1.0535 0.3159
## Residuals 22 0.152146 0.0069157## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.15592 0.09912 2.4205 0.066 .
## Residual 22 1.41714 0.90088
## Total 23 1.57305 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Cecum bray data..."
## $sites
## PCoA1 PCoA2
## c1_C21R08 -0.32970276 0.13961184
## c1_C21R12 -0.20023921 0.04888849
## c1_C21R24 -0.35418723 0.17346596
## c1_C21R33 0.23766201 -0.02418866
## c1_C21R34 0.39312098 0.10969205
## c1_C21R44 0.25621158 0.01048271
## c1_C8R03 -0.31842817 0.25068642
## c1_C8R16 -0.30107344 0.19829288
## c1_C8R28 -0.03692354 -0.07421843
## c2_C21R11 -0.32022018 0.13576958
## c2_C21R19 -0.25217134 0.04296908
## c2_C21R20 -0.26376037 0.12300298
## c2_C21R22 -0.26237260 0.01963181
## c2_C21R23 -0.26609644 0.02652681
## c2_C21R32 0.15237607 -0.18364481
## c2_C21R36 0.12281182 -0.25940642
## c2_C21R45 -0.02930299 -0.28828664
## c2_C21R46 0.49629474 0.28171438
## c2_C21R48 0.43176358 0.30191306
## c2_C8R02 -0.29839071 0.12593368
## c2_C8R05 -0.27933778 0.24610699
## c2_C8R06 -0.24678039 0.15251740
## c2_C8R42 0.36317864 0.01111843
## c3_C21R07 -0.26223574 -0.08637904
## c3_C21R09 -0.21537394 -0.15748649
## c3_C21R10 -0.16734468 -0.19177055
## c3_C21R31 0.41485059 0.27135631
## c3_C21R35 0.40535993 0.13167359
## c3_C21R43 -0.03526921 -0.36505024
## c3_C8R01 -0.28777189 0.04678440
## c3_C8R14 -0.28575244 0.06401528
## c3_C8R15 -0.27708982 0.15531046
## c3_C8R25 0.36481275 0.15579112
## c3_C8R27 0.40292896 0.18366513
## c3_C8R29 0.42021700 0.05020574
## c3_C8R37 -0.02457899 -0.35790965
## c3_C8R38 0.02079955 -0.43311876
## c3_C8R39 0.28583633 -0.29812061
## c3_C8R41 0.16765343 -0.37800502
## c4_C21R21 -0.12065048 -0.05794281
## c4_C21R47 0.03237171 -0.37462550
## c4_C8R13 -0.24257519 0.03916718
## c4_C8R17 -0.13304126 0.12232833
## c4_C8R18 -0.04202865 -0.02198851
## c4_C8R26 0.39016029 0.10076266
## c4_C8R30 0.44676775 0.09240383
## c4_C8R40 0.04752173 -0.25964643
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.28577944 0.003627569
## 21_HF_PFOS 0.25299450 -0.072430049
## 21_LF_CTRL -0.25138979 -0.031866119
## 21_LF_PFOS -0.25971182 0.053959923
## 8_HF_CTRL 0.37402288 0.092022633
## 8_HF_PFOS 0.06890639 -0.324947892
## 8_LF_CTRL -0.28767122 0.160589160
## 8_LF_PFOS -0.23096395 0.097374658
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.10621 0.015173 0.9124 0.5072
## Residuals 39 0.64857 0.016630## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.4083 0.03424 2.3202 0.020 *
## feed 1 3.0897 0.25908 17.5568 0.001 ***
## PFOS 1 0.3129 0.02624 1.7782 0.093 .
## day:feed 1 0.2955 0.02478 1.6794 0.088 .
## day:PFOS 1 0.2711 0.02273 1.5404 0.114
## feed:PFOS 1 0.4245 0.03559 2.4120 0.022 *
## day:feed:PFOS 1 0.2601 0.02181 1.4779 0.134
## Residual 39 6.8632 0.57552
## Total 46 11.9253 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Cecum jac data..."
## $sites
## PCoA1 PCoA2
## c1_C21R08 -0.165707630 -0.225651909
## c1_C21R12 -0.155631358 -0.227460061
## c1_C21R24 -0.209795667 -0.261928391
## c1_C21R33 0.091582434 -0.301991416
## c1_C21R34 0.101855504 -0.311051486
## c1_C21R44 0.230134094 -0.290934267
## c1_C8R03 -0.100834832 -0.247620137
## c1_C8R16 -0.153145946 -0.237216744
## c1_C8R28 -0.002173878 -0.292176139
## c2_C21R11 -0.211793376 -0.002710398
## c2_C21R19 -0.191046089 0.020718285
## c2_C21R20 -0.177845653 -0.008702169
## c2_C21R22 -0.205207165 0.003564039
## c2_C21R23 -0.194318074 -0.001808959
## c2_C21R32 0.084184954 -0.011918374
## c2_C21R36 -0.023912244 0.009872217
## c2_C21R45 -0.055341601 0.008667246
## c2_C21R46 0.287588218 -0.088668479
## c2_C21R48 0.264881480 -0.124935054
## c2_C8R02 -0.179062731 0.015379813
## c2_C8R05 -0.151840350 -0.036708876
## c2_C8R06 -0.199188676 0.008555422
## c2_C8R42 0.057617611 -0.038420577
## c3_C21R07 -0.108306830 0.195940772
## c3_C21R09 -0.079863677 0.196590488
## c3_C21R10 -0.071490418 0.173915636
## c3_C21R31 0.326124097 0.014755689
## c3_C21R35 0.305338557 0.029117460
## c3_C21R43 -0.004336082 0.176912309
## c3_C8R01 -0.069423701 0.208218013
## c3_C8R14 -0.070787153 0.177232946
## c3_C8R15 -0.030598765 0.192247683
## c3_C8R25 0.123783807 0.132737238
## c3_C8R27 0.329392439 0.080990146
## c3_C8R29 0.270539144 0.055523741
## c3_C8R37 0.042231610 0.175592273
## c3_C8R38 0.062348609 0.160053034
## c3_C8R39 0.150685960 0.141932857
## c3_C8R41 0.157620457 0.111933290
## c4_C21R21 -0.120488714 0.091230998
## c4_C21R47 -0.020484908 0.046860944
## c4_C8R13 -0.143860468 0.083818331
## c4_C8R17 -0.112447396 0.070879389
## c4_C8R18 -0.113420295 0.074702410
## c4_C8R26 0.186188779 0.010612334
## c4_C8R30 0.297056626 -0.013363842
## c4_C8R40 -0.046800704 0.054712275
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.14257949 -0.099212369
## 21_HF_PFOS 0.10860253 -0.012502305
## 21_LF_CTRL -0.12864468 0.040575086
## 21_LF_PFOS -0.18631767 -0.014457366
## 8_HF_CTRL 0.21567607 0.011670126
## 8_HF_PFOS 0.06500292 0.107164862
## 8_LF_CTRL -0.15134764 -0.000756063
## 8_LF_PFOS -0.10367757 0.070831302
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.041308 0.0059011 0.9703 0.4662
## Residuals 39 0.237182 0.0060816## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.2477 0.03085 1.6797 0.033 *
## feed 1 1.0396 0.12952 7.0511 0.001 ***
## PFOS 1 0.1921 0.02393 1.3028 0.142
## day:feed 1 0.1624 0.02023 1.1011 0.290
## day:PFOS 1 0.2231 0.02780 1.5134 0.080 .
## feed:PFOS 1 0.2124 0.02646 1.4404 0.103
## day:feed:PFOS 1 0.1992 0.02481 1.3508 0.145
## Residual 39 5.7503 0.71639
## Total 46 8.0267 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Cecum unif data..."
## $sites
## PCoA1 PCoA2
## c1_C21R08 0.093660263 -0.153445552
## c1_C21R12 0.134833748 -0.098685673
## c1_C21R24 0.141396652 -0.161641895
## c1_C21R33 -0.128538545 -0.169849086
## c1_C21R34 -0.104699837 -0.158604910
## c1_C21R44 -0.169694876 -0.063333354
## c1_C8R03 0.039614915 -0.087628856
## c1_C8R16 0.078070352 -0.147943696
## c1_C8R28 -0.043547126 -0.175804302
## c2_C21R11 0.174901679 0.001592616
## c2_C21R19 0.109014468 0.077040377
## c2_C21R20 0.101987532 0.060610190
## c2_C21R22 0.143964529 0.037925772
## c2_C21R23 0.107279199 0.030691957
## c2_C21R32 -0.143064489 -0.002283716
## c2_C21R36 -0.002732195 -0.017102739
## c2_C21R45 -0.025178488 -0.029859404
## c2_C21R46 -0.199146211 0.088871569
## c2_C21R48 -0.171325374 0.014112957
## c2_C8R02 0.116765631 0.062197014
## c2_C8R05 0.129534432 0.056131313
## c2_C8R06 0.119206352 0.019611072
## c2_C8R42 -0.079002473 -0.073196395
## c3_C21R07 0.142613623 0.013507705
## c3_C21R09 0.049016711 0.013798238
## c3_C21R10 0.096636845 0.027739364
## c3_C21R31 -0.177627406 0.035164201
## c3_C21R35 -0.194779622 0.093598092
## c3_C21R43 0.008970713 -0.059127907
## c3_C8R01 0.095369642 0.036555531
## c3_C8R14 0.096202110 0.027178239
## c3_C8R15 0.074084627 0.034194087
## c3_C8R25 -0.084806667 -0.072100029
## c3_C8R27 -0.215653126 0.079881019
## c3_C8R29 -0.170413412 0.043799368
## c3_C8R37 -0.034669902 -0.047709395
## c3_C8R38 -0.030450683 -0.049790008
## c3_C8R39 -0.091209707 -0.037157715
## c3_C8R41 -0.102939333 -0.027362597
## c4_C21R21 0.109486677 0.121801341
## c4_C21R47 -0.034033512 0.003098462
## c4_C8R13 0.140044716 0.096836592
## c4_C8R17 0.086222962 0.100261200
## c4_C8R18 0.098660138 0.116011125
## c4_C8R26 -0.090397797 0.160160573
## c4_C8R30 -0.188644634 0.162123476
## c4_C8R40 -0.004983104 0.018133780
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL -0.12515690 -0.04115558
## 21_HF_PFOS -0.09725010 -0.01061828
## 21_LF_CTRL 0.11813238 -0.02795447
## 21_LF_PFOS 0.11731469 0.03634597
## 8_HF_CTRL -0.14108911 0.04122639
## 8_HF_PFOS -0.04699952 -0.04121923
## 8_LF_CTRL 0.10553710 0.02623247
## 8_LF_PFOS 0.09639094 0.04332208
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.024146 0.0034494 1.3964 0.2345
## Residuals 39 0.096339 0.0024702## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.07509 0.02488 1.4438 0.121
## feed 1 0.56479 0.18713 10.8591 0.001 ***
## PFOS 1 0.06503 0.02155 1.2503 0.211
## day:feed 1 0.06025 0.01996 1.1584 0.269
## day:PFOS 1 0.07452 0.02469 1.4329 0.124
## feed:PFOS 1 0.08373 0.02774 1.6099 0.063 .
## day:feed:PFOS 1 0.06640 0.02200 1.2766 0.194
## Residual 39 2.02842 0.67205
## Total 46 3.01824 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Cecum wuf data..."
## $sites
## PCoA1 PCoA2
## c1_C21R08 -0.275004404 -0.0946650033
## c1_C21R12 0.129404281 -0.3504934647
## c1_C21R24 -0.237272152 -0.1350513652
## c1_C21R33 -0.174164425 -0.1407999403
## c1_C21R34 -0.331110423 0.0117893531
## c1_C21R44 0.129464909 -0.3144399128
## c1_C8R03 -0.289237918 -0.1408827366
## c1_C8R16 -0.457050817 0.0024263114
## c1_C8R28 -0.006793177 -0.2162050360
## c2_C21R11 -0.199989962 0.0091490522
## c2_C21R19 0.085444393 0.0305420684
## c2_C21R20 -0.098671477 -0.0008476165
## c2_C21R22 0.094384589 0.0197548174
## c2_C21R23 0.069363092 -0.0475262592
## c2_C21R32 0.054662610 0.0802562941
## c2_C21R36 0.180004859 0.0350305034
## c2_C21R45 0.183134679 -0.0485351826
## c2_C21R46 -0.287778115 0.1269584426
## c2_C21R48 -0.470929050 0.0850490677
## c2_C8R02 -0.116250802 0.0333604384
## c2_C8R05 -0.140294080 -0.1461887202
## c2_C8R06 -0.046871053 -0.0278094369
## c2_C8R42 -0.015245948 0.0686214389
## c3_C21R07 0.116184883 0.0089735186
## c3_C21R09 0.192936318 0.0309893736
## c3_C21R10 0.249227587 -0.0267961054
## c3_C21R31 -0.432816186 0.0880924434
## c3_C21R35 0.097562555 0.1392814321
## c3_C21R43 0.262242872 0.1658880720
## c3_C8R01 -0.116974863 -0.0544059336
## c3_C8R14 -0.118701951 0.0567108915
## c3_C8R15 -0.069458891 -0.0144228169
## c3_C8R25 -0.423462863 0.1232737849
## c3_C8R27 -0.098579656 0.1539532796
## c3_C8R29 0.052888401 0.0608654627
## c3_C8R37 0.234730134 0.1599119280
## c3_C8R38 0.265443141 0.1813444178
## c3_C8R39 0.130204423 0.1404031246
## c3_C8R41 0.250994208 0.0774955548
## c4_C21R21 0.284265494 -0.0352044610
## c4_C21R47 0.368239677 0.1183440373
## c4_C8R13 0.024939623 0.1041050209
## c4_C8R17 0.220277512 -0.0011135433
## c4_C8R18 0.267880499 -0.3571041305
## c4_C8R26 0.143310709 0.0257814951
## c4_C8R30 0.177686037 -0.0118071096
## c4_C8R40 0.141780730 0.0259471503
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL -0.07733961 0.031337886
## 21_HF_PFOS 0.04840190 0.062747720
## 21_LF_CTRL 0.08373850 -0.034885000
## 21_LF_PFOS 0.05459104 -0.018985451
## 8_HF_CTRL 0.03022279 0.035659629
## 8_HF_PFOS 0.21737775 0.126164325
## 8_LF_CTRL -0.12654017 -0.051958697
## 8_LF_PFOS -0.03712286 0.007223564
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.11623 0.016604 0.8163 0.5794
## Residuals 39 0.79325 0.020340## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.0778 0.01580 0.8335 0.533
## feed 1 0.5625 0.11430 6.0286 0.001 ***
## PFOS 1 0.1879 0.03819 2.0143 0.093 .
## day:feed 1 0.2255 0.04581 2.4163 0.062 .
## day:PFOS 1 0.0954 0.01939 1.0225 0.359
## feed:PFOS 1 0.0803 0.01633 0.8611 0.478
## day:feed:PFOS 1 0.0528 0.01073 0.5659 0.692
## Residual 39 3.6389 0.73944
## Total 46 4.9212 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Cecum_HF bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_C21R33 0.02424541 -0.15725088
## c1_C21R34 0.20374841 0.14773610
## c1_C21R44 0.08953876 -0.39692509
## c1_C8R28 -0.20103713 -0.20085282
## c2_C21R32 -0.16747849 -0.03262366
## c2_C21R36 -0.22524935 -0.11408917
## c2_C21R45 -0.33198873 -0.13771417
## c2_C21R46 0.43711461 0.13404122
## c2_C21R48 0.40595951 0.25328827
## c2_C8R42 0.13930911 -0.06252887
## c3_C21R31 0.37766083 0.24684396
## c3_C21R35 0.27528248 -0.09862903
## c3_C21R43 -0.41165649 0.18427236
## c3_C8R25 0.25434062 0.34324666
## c3_C8R27 0.31124376 0.06442294
## c3_C8R29 0.22569090 -0.13733257
## c3_C8R37 -0.40981238 0.21062662
## c3_C8R38 -0.44188487 0.21666883
## c3_C8R39 -0.14990433 0.08719445
## c3_C8R41 -0.27612442 -0.02628402
## c4_C21R47 -0.35005782 0.03497359
## c4_C8R26 0.23773976 -0.20983460
## c4_C8R30 0.26346065 -0.32215700
## c4_C8R40 -0.28014080 -0.02709311
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.075489299 0.0005909707
## 21_HF_PFOS 0.008577305 0.0206000373
## 8_HF_CTRL 0.219252192 -0.1008666013
## 8_HF_PFOS -0.318180701 0.1124775799
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.01968 0.0065586 0.3001 0.8249
## Residuals 20 0.43713 0.0218566## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.2684 0.05100 1.3139 0.235
## PFOS 1 0.5861 0.11136 2.8689 0.021 *
## day:PFOS 1 0.3229 0.06135 1.5806 0.155
## Residual 20 4.0856 0.77630
## Total 23 5.2630 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Cecum_HF jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_C21R33 0.069505629 -0.315035653
## c1_C21R34 0.102905740 -0.294694892
## c1_C21R44 0.272352701 -0.176371320
## c1_C8R28 -0.003200288 -0.322954536
## c2_C21R32 -0.015148744 -0.046055076
## c2_C21R36 -0.115295723 -0.100679421
## c2_C21R45 -0.165547695 -0.089644417
## c2_C21R46 0.258596585 0.013455995
## c2_C21R48 0.245498373 -0.001344125
## c2_C8R42 -0.056739069 -0.097460408
## c3_C21R31 0.157031917 0.214580384
## c3_C21R35 0.184583669 0.190950408
## c3_C21R43 -0.269850387 0.066443122
## c3_C8R25 -0.197890140 0.157447911
## c3_C8R27 0.154355181 0.237819748
## c3_C8R29 0.130583401 0.163620190
## c3_C8R37 -0.285825955 0.075673724
## c3_C8R38 -0.248045018 0.097773394
## c3_C8R39 -0.159656355 0.128971845
## c3_C8R41 -0.153775084 0.100467233
## c4_C21R47 -0.173159441 -0.094898287
## c4_C8R26 0.156482679 0.067166744
## c4_C8R30 0.279731513 0.099717951
## c4_C8R40 -0.167493487 -0.074950512
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.06040176 -0.06714401
## 21_HF_PFOS -0.01991606 -0.03245136
## 8_HF_CTRL 0.10027752 0.09036540
## 8_HF_PFOS -0.18700658 0.04937329
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.00758 0.0025266 0.3427 0.7948
## Residuals 20 0.14747 0.0073737## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.2445 0.06084 1.4677 0.092 .
## PFOS 1 0.2610 0.06495 1.5670 0.052 .
## day:PFOS 1 0.1817 0.04521 1.0907 0.345
## Residual 20 3.3313 0.82900
## Total 23 4.0184 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Cecum_HF unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_C21R33 0.026908827 -0.208838732
## c1_C21R34 0.001995097 -0.160888197
## c1_C21R44 -0.120077149 -0.167699752
## c1_C8R28 0.085323537 -0.213685947
## c2_C21R32 -0.068902716 0.063640687
## c2_C21R36 0.077671397 0.019287587
## c2_C21R45 0.151434011 0.018981685
## c2_C21R46 -0.151001457 0.035693006
## c2_C21R48 -0.149658865 -0.005204363
## c2_C8R42 0.094855714 0.005856955
## c3_C21R31 -0.168348261 0.016265804
## c3_C21R35 -0.157699078 0.049938924
## c3_C21R43 0.136172007 0.016976108
## c3_C8R25 0.093686338 0.013922000
## c3_C8R27 -0.173447308 0.072000898
## c3_C8R29 -0.143836786 0.040485057
## c3_C8R37 0.194567027 0.077851036
## c3_C8R38 0.157986480 0.086460294
## c3_C8R39 0.103755064 0.032554305
## c3_C8R41 0.088525498 0.061776375
## c4_C21R47 0.109831528 0.052668614
## c4_C8R26 -0.132548247 0.062701377
## c4_C8R30 -0.172229240 0.017681954
## c4_C8R40 0.115036582 0.011574328
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL -0.04880514 -0.03762314
## 21_HF_PFOS 0.03927114 0.02850800
## 8_HF_CTRL -0.09360439 0.01329063
## 8_HF_PFOS 0.12059473 0.02945015
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.002044 0.0006813 0.2134 0.8859
## Residuals 20 0.063865 0.0031932## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.09194 0.06106 1.5029 0.108
## PFOS 1 0.12709 0.08441 2.0775 0.026 *
## day:PFOS 1 0.06308 0.04190 1.0311 0.371
## Residual 20 1.22351 0.81263
## Total 23 1.50563 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Cecum_HF wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_C21R33 -0.176922062 -0.204158743
## c1_C21R34 -0.341754582 -0.031810596
## c1_C21R44 0.081523372 -0.371449705
## c1_C8R28 -0.001036853 -0.298791088
## c2_C21R32 0.054454035 -0.000260074
## c2_C21R36 0.166049522 -0.020597232
## c2_C21R45 0.171645415 -0.106145047
## c2_C21R46 -0.320260045 0.086904436
## c2_C21R48 -0.508751622 0.078256106
## c2_C8R42 -0.033404789 -0.015302757
## c3_C21R31 -0.466171161 0.080379758
## c3_C21R35 0.071042468 0.062193116
## c3_C21R43 0.262753250 0.175108777
## c3_C8R25 -0.448216943 0.115362590
## c3_C8R27 -0.112329027 0.106525102
## c3_C8R29 0.022422242 -0.028333119
## c3_C8R37 0.230989330 0.150653968
## c3_C8R38 0.256722839 0.189227859
## c3_C8R39 0.116763830 0.073511668
## c3_C8R41 0.235361720 0.033632113
## c4_C21R47 0.352460993 0.148297359
## c4_C8R26 0.109223535 -0.053723725
## c4_C8R30 0.134907622 -0.130596198
## c4_C8R40 0.142526912 -0.038884566
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL -0.091857859 -0.02891661
## 21_HF_PFOS 0.029427743 0.01494978
## 8_HF_CTRL 0.003486677 -0.04354998
## 8_HF_PFOS 0.212034926 0.11122399
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.02498 0.008326 0.3593 0.783
## Residuals 20 0.46340 0.023170## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.13094 0.05094 1.2220 0.268
## PFOS 1 0.23099 0.08987 2.1557 0.098 .
## day:PFOS 1 0.06541 0.02545 0.6104 0.654
## Residual 20 2.14301 0.83374
## Total 23 2.57035 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Cecum_LF bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_C21R08 0.20052211 0.194737604
## c1_C21R12 -0.27378343 0.023730634
## c1_C21R24 0.15585905 0.009645821
## c1_C8R03 0.23225535 -0.261934385
## c1_C8R16 0.35948111 0.018675319
## c2_C21R11 0.18578711 0.101104752
## c2_C21R19 -0.04470625 0.132925659
## c2_C21R20 0.06156701 -0.049218905
## c2_C21R22 -0.05338040 0.173858007
## c2_C21R23 -0.10303156 0.090420688
## c2_C8R02 0.15775354 -0.037490042
## c2_C8R05 0.12794090 -0.300923707
## c2_C8R06 0.12676688 -0.110415634
## c3_C21R07 -0.07097538 0.285823179
## c3_C21R09 -0.17575663 0.191473026
## c3_C21R10 -0.23361529 0.172497131
## c3_C8R01 0.04364500 0.009944979
## c3_C8R14 0.12960463 0.102830975
## c3_C8R15 0.10896921 -0.219599232
## c4_C21R21 -0.33548206 -0.113293974
## c4_C8R13 0.04038720 0.109052963
## c4_C8R17 -0.15817673 -0.318571064
## c4_C8R18 -0.48163134 -0.205273794
##
## $centroids
## PCoA1 PCoA2
## 21_LF_CTRL -0.05424792 0.17844998
## 21_LF_PFOS -0.04810861 0.06160483
## 8_LF_CTRL 0.13916561 -0.13004419
## 8_LF_PFOS 0.03645204 -0.07019862
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.043644 0.014548 1.3154 0.2986
## Residuals 19 0.210134 0.011060## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.4347 0.12148 2.9733 0.002 **
## PFOS 1 0.1675 0.04681 1.1456 0.291
## day:PFOS 1 0.1983 0.05541 1.3563 0.172
## Residual 19 2.7776 0.77630
## Total 22 3.5780 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Cecum_LF jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_C21R08 -0.328705162 -0.08207436
## c1_C21R12 -0.290080954 -0.07869047
## c1_C21R24 -0.311619458 -0.08526226
## c1_C8R03 -0.315188221 -0.08146541
## c1_C8R16 -0.305331630 -0.05735585
## c2_C21R11 -0.002967032 0.11438187
## c2_C21R19 0.058157366 0.12661612
## c2_C21R20 0.012498800 0.12239582
## c2_C21R22 0.022804499 0.11030439
## c2_C21R23 0.028446709 0.09736255
## c2_C8R02 0.011822351 0.10851238
## c2_C8R05 -0.018000066 0.14665028
## c2_C8R06 -0.002607562 0.12229643
## c3_C21R07 0.142474256 -0.22047723
## c3_C21R09 0.179886316 -0.19300433
## c3_C21R10 0.184200561 -0.18433952
## c3_C8R01 0.183799218 -0.18997082
## c3_C8R14 0.161630332 -0.23622970
## c3_C8R15 0.154088688 -0.21278218
## c4_C21R21 0.135027894 0.19057894
## c4_C8R13 0.095443998 0.13950600
## c4_C8R17 0.084752879 0.16667722
## c4_C8R18 0.119466216 0.17637015
##
## $centroids
## PCoA1 PCoA2
## 21_LF_CTRL 0.01994275 -0.11981808
## 21_LF_PFOS 0.01147623 0.10434571
## 8_LF_CTRL -0.01749119 0.05461252
## 8_LF_PFOS 0.06617622 0.00775153
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.018948 0.0063161 0.7935 0.5125
## Residuals 19 0.151241 0.0079601## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.12941 0.04720 1.0886 0.365
## PFOS 1 0.15193 0.05541 1.2780 0.203
## day:PFOS 1 0.20175 0.07358 1.6970 0.068 .
## Residual 19 2.25875 0.82381
## Total 22 2.74183 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Cecum_LF unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_C21R08 -0.22231507 -0.010389681
## c1_C21R12 -0.12835603 -0.026856335
## c1_C21R24 -0.16141080 0.036605760
## c1_C8R03 -0.18545604 -0.031093485
## c1_C8R16 -0.19865724 0.019938143
## c2_C21R11 0.01131651 0.086455223
## c2_C21R19 0.09510601 0.087597386
## c2_C21R20 0.04616660 0.099983483
## c2_C21R22 0.03101281 0.056551370
## c2_C21R23 0.04301176 0.048861131
## c2_C8R02 0.03591362 0.026670683
## c2_C8R05 -0.01530095 0.070237970
## c2_C8R06 0.04344375 0.030578532
## c3_C21R07 0.04770021 -0.114734424
## c3_C21R09 0.03999154 -0.076949255
## c3_C21R10 0.03130901 -0.063977764
## c3_C8R01 0.02583485 -0.051911788
## c3_C8R14 0.05851822 -0.116072966
## c3_C8R15 0.03633834 -0.077462150
## c4_C21R21 0.12597277 0.020168406
## c4_C8R13 0.08187812 -0.054029643
## c4_C8R17 0.06981787 0.042136429
## c4_C8R18 0.08816414 -0.002307025
##
## $centroids
## PCoA1 PCoA2
## 21_LF_CTRL -0.023379768 -0.03603151
## 21_LF_PFOS 0.041912978 0.06310598
## 8_LF_CTRL -0.005636911 0.01619263
## 8_LF_PFOS 0.037426532 -0.03941864
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.003609 0.0012030 0.604 0.6204
## Residuals 19 0.037846 0.0019919## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.04456 0.05212 1.1839 0.254
## PFOS 1 0.05189 0.06068 1.3784 0.154
## day:PFOS 1 0.04339 0.05074 1.1526 0.287
## Residual 19 0.71518 0.83646
## Total 22 0.85501 1.00000
## [1] ""
## [1] "Processing Cecum_LF wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_C21R08 0.243001251 0.08089244
## c1_C21R12 -0.233467694 0.31378302
## c1_C21R24 0.203077752 0.08302824
## c1_C8R03 0.253336637 0.15220528
## c1_C8R16 0.428745736 0.08978070
## c2_C21R11 0.192566381 -0.01745948
## c2_C21R19 -0.079842513 -0.10626278
## c2_C21R20 0.097039903 -0.04737135
## c2_C21R22 -0.091874353 -0.12806061
## c2_C21R23 -0.083948145 -0.05060673
## c2_C8R02 0.119034487 -0.05544333
## c2_C8R05 0.110887581 0.08409841
## c2_C8R06 0.044498242 -0.02608847
## c3_C21R07 -0.114032964 -0.11326828
## c3_C21R09 -0.188284340 -0.10938888
## c3_C21R10 -0.268539648 -0.04316097
## c3_C8R01 0.099400180 0.01998541
## c3_C8R14 0.130701053 -0.09841100
## c3_C8R15 0.068427967 -0.04709579
## c4_C21R21 -0.314252311 -0.06739999
## c4_C8R13 -0.003149804 -0.18225286
## c4_C8R17 -0.229278095 -0.05207597
## c4_C8R18 -0.384047302 0.32057301
##
## $centroids
## PCoA1 PCoA2
## 21_LF_CTRL -0.10131884 -0.03145227
## 21_LF_PFOS -0.06370998 -0.06798629
## 8_LF_CTRL 0.11375886 0.01785261
## 8_LF_PFOS 0.03483143 -0.05332768
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.06613 0.022044 1.2984 0.3039
## Residuals 19 0.32256 0.016977## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.16535 0.09290 2.1109 0.116
## PFOS 1 0.04717 0.02650 0.6023 0.661
## day:PFOS 1 0.07909 0.04444 1.0098 0.388
## Residual 19 1.48824 0.83616
## Total 22 1.77986 1.00000
## [1] ""## [1] "Processing Ileum bray data..."## Warning in betadisper(dist.used, mdat[, VAR]): some squared distances are
## negative and changed to zero
## $sites
## PCoA1 PCoA2
## c1_Il21R10 -0.05828663 0.073907155
## c1_Il21R20 -0.24883449 0.039775341
## c1_Il21R22 -0.35020740 0.027723211
## c1_Il21R24 -0.43311416 0.084716195
## c1_Il21R32 -0.03468749 -0.208908838
## c1_Il21R44 0.35121098 0.145812127
## c1_Il21R48 -0.16678172 0.023751453
## c1_Il8R14 -0.41951372 0.078235877
## c1_Il8R29 0.38019130 0.119534531
## c1_Il8R37 0.49584555 0.115690761
## c2_Il21R09 -0.17318981 0.043871691
## c2_Il21R21 -0.42574029 0.077405818
## c2_Il21R31 0.33041669 -0.271212618
## c2_Il21R33 0.27244009 -0.231423355
## c2_Il21R36 0.15329893 -0.094810634
## c2_Il21R43 -0.04639938 -0.138941090
## c2_Il21R45 0.05723125 -0.088584303
## c2_Il8R03 0.25240557 -0.082151786
## c2_Il8R18 -0.38641459 0.058386666
## c2_Il8R28 0.51167407 0.250592873
## c2_Il8R30 0.47111309 0.210661533
## c3_Il21R07 -0.33235232 0.039615460
## c3_Il21R08 -0.38684462 0.053375384
## c3_Il21R11 -0.31552201 0.040119171
## c3_Il21R35 0.39706949 0.125873178
## c3_Il8R05 -0.18080977 -0.042999665
## c3_Il8R13 -0.41520046 0.058898098
## c3_Il8R16 -0.35315143 0.052545928
## c3_Il8R25 0.18111462 -0.340319570
## c3_Il8R26 0.29449045 -0.319906647
## c3_Il8R38 0.11376411 0.085312279
## c3_Il8R41 0.08892580 -0.006054764
## c3_Il8R42 0.49136878 0.238524052
## c4_Il21R19 -0.39541284 0.051285680
## c4_Il21R23 -0.37983510 0.030490607
## c4_Il21R34 0.18826495 -0.192869270
## c4_Il21R46 0.43797474 0.193181249
## c4_Il21R47 -0.24898418 -0.164996295
## c4_Il8R01 -0.36295707 0.003901650
## c4_Il8R02 -0.26779527 0.001228919
## c4_Il8R06 0.30624177 0.069350986
## c4_Il8R17 -0.07370637 0.035762809
## c4_Il8R27 0.34988559 -0.183573201
## c4_Il8R39 0.25151395 0.083378791
## c4_Il8R40 0.07929934 -0.146157437
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.21687106 -0.152927450
## 21_HF_PFOS 0.08145959 -0.004882776
## 21_LF_CTRL -0.27709219 0.046433499
## 21_LF_PFOS -0.37997790 0.058054928
## 8_HF_CTRL 0.39287373 0.045508548
## 8_HF_PFOS 0.23636359 0.060503734
## 8_LF_CTRL -0.13363293 -0.019083467
## 8_LF_PFOS -0.36436409 0.059348165
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.19805 0.028292 1.1306 0.3654
## Residuals 37 0.92588 0.025024## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.2715 0.03748 2.8551 0.060 .
## feed 1 2.6603 0.36725 27.9764 0.001 ***
## PFOS 1 0.4138 0.05712 4.3515 0.018 *
## day:feed 1 0.1114 0.01538 1.1719 0.264
## day:PFOS 1 0.0650 0.00898 0.6838 0.508
## feed:PFOS 1 0.0668 0.00922 0.7020 0.491
## day:feed:PFOS 1 0.1367 0.01888 1.4379 0.198
## Residual 37 3.5184 0.48570
## Total 44 7.2439 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Ileum jac data..."## Warning in MASS::cov.trob(data[, vars]): Probable convergence failure## Warning in MASS::cov.trob(data[, vars]): Probable convergence failure
## $sites
## PCoA1 PCoA2
## c1_Il21R10 -0.31837382 -0.2130068393
## c1_Il21R20 -0.32603404 -0.2141883728
## c1_Il21R22 -0.24752571 -0.1716822998
## c1_Il21R24 -0.37394996 -0.1565775790
## c1_Il21R32 0.01995386 -0.3260896629
## c1_Il21R44 0.09128491 -0.3780686756
## c1_Il21R48 0.01658859 -0.3623509668
## c1_Il8R14 -0.09972643 -0.2840923532
## c1_Il8R29 -0.28952510 -0.3062146723
## c1_Il8R37 -0.26212209 -0.1599047015
## c2_Il21R09 -0.12481429 0.1444267189
## c2_Il21R21 -0.11840544 0.1871129829
## c2_Il21R31 0.26986690 -0.0723278346
## c2_Il21R33 0.15489230 0.0929317577
## c2_Il21R36 -0.09266312 0.0998468042
## c2_Il21R43 0.15602134 0.0502271146
## c2_Il21R45 0.15350884 0.0820472088
## c2_Il8R03 0.24214762 0.0270569451
## c2_Il8R18 -0.26044547 0.2014321576
## c2_Il8R28 0.30960357 -0.1057651017
## c2_Il8R30 0.22914415 -0.0859957026
## c3_Il21R07 -0.02677449 0.1570890083
## c3_Il21R08 0.25287619 0.0009834736
## c3_Il21R11 0.19679349 0.0463183029
## c3_Il21R35 0.04495658 0.0182878342
## c3_Il8R05 0.15551082 0.0467984347
## c3_Il8R13 -0.22194417 0.2362464875
## c3_Il8R16 -0.08326994 0.1564614431
## c3_Il8R25 0.06596362 0.0291978214
## c3_Il8R26 -0.09131972 0.0720039355
## c3_Il8R38 -0.11931873 0.1558027791
## c3_Il8R41 0.09548227 0.0901003505
## c3_Il8R42 0.07818134 0.0310483788
## c4_Il21R19 0.25747541 0.0006441430
## c4_Il21R23 0.33529792 -0.0340415520
## c4_Il21R34 0.25406132 0.0305115161
## c4_Il21R46 -0.27530551 0.1418499698
## c4_Il21R47 0.34400409 -0.0833825234
## c4_Il8R01 0.07309523 0.0984284948
## c4_Il8R02 -0.13380179 0.1825465115
## c4_Il8R06 0.07768672 0.0633809403
## c4_Il8R17 -0.18013096 0.1840646710
## c4_Il8R27 -0.08232411 0.0837592241
## c4_Il8R39 0.04900830 0.0714370121
## c4_Il8R40 -0.19563050 0.1716464153
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.11474972 -0.023735341
## 21_HF_PFOS 0.07110762 -0.007052935
## 21_LF_CTRL 0.02678326 0.047007309
## 21_LF_PFOS -0.11966836 -0.084246587
## 8_HF_CTRL 0.03658991 -0.037617883
## 8_HF_PFOS -0.05857617 0.002139573
## 8_LF_CTRL 0.08936892 0.080258559
## 8_LF_PFOS -0.17818450 0.129614396
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.044927 0.0064182 1.1338 0.3636
## Residuals 37 0.209452 0.0056609## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.2348 0.02254 1.0180 0.361
## feed 1 0.4519 0.04339 1.9595 0.014 *
## PFOS 1 0.2830 0.02718 1.2271 0.171
## day:feed 1 0.2545 0.02444 1.1035 0.261
## day:PFOS 1 0.2176 0.02089 0.9435 0.519
## feed:PFOS 1 0.2100 0.02016 0.9105 0.567
## day:feed:PFOS 1 0.2292 0.02201 0.9937 0.399
## Residual 37 8.5338 0.81938
## Total 44 10.4148 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Ileum unif data..."
## $sites
## PCoA1 PCoA2
## c1_Il21R10 -0.18806001 0.074858298
## c1_Il21R20 -0.21572272 -0.143222086
## c1_Il21R22 -0.19734469 -0.115971852
## c1_Il21R24 -0.38448803 0.029166748
## c1_Il21R32 0.08003299 -0.151777238
## c1_Il21R44 0.15478814 -0.177182646
## c1_Il21R48 0.07861421 -0.167124299
## c1_Il8R14 0.02347659 -0.189087131
## c1_Il8R29 -0.29882651 -0.061261849
## c1_Il8R37 -0.12712078 -0.060704969
## c2_Il21R09 -0.12510498 -0.045859096
## c2_Il21R21 -0.23722980 -0.012844265
## c2_Il21R31 0.18371744 -0.077612302
## c2_Il21R33 0.15508218 0.194990716
## c2_Il21R36 -0.11692376 -0.030213811
## c2_Il21R43 0.09932717 -0.051703521
## c2_Il21R45 0.09333366 0.140413200
## c2_Il8R03 0.19245684 -0.059895175
## c2_Il8R18 -0.30038757 0.076117857
## c2_Il8R28 0.27769254 0.003753552
## c2_Il8R30 0.18406465 -0.055151158
## c3_Il21R07 -0.07943846 0.098114914
## c3_Il21R08 0.24788033 -0.039029808
## c3_Il21R11 0.19676793 0.008879315
## c3_Il21R35 0.04637354 -0.083822582
## c3_Il8R05 0.14809329 -0.075638536
## c3_Il8R13 -0.26911916 0.057488600
## c3_Il8R16 -0.09543563 0.050786845
## c3_Il8R25 0.08787822 0.017474153
## c3_Il8R26 -0.06953188 0.158312898
## c3_Il8R38 -0.06986609 0.070585588
## c3_Il8R41 0.13421728 0.026037251
## c3_Il8R42 0.10383370 -0.022363707
## c4_Il21R19 0.23252960 0.029242616
## c4_Il21R23 0.29998735 0.068116862
## c4_Il21R34 0.23733188 0.079784048
## c4_Il21R46 -0.29657860 -0.043206361
## c4_Il21R47 0.31559697 0.115216233
## c4_Il8R01 0.06991922 0.022736040
## c4_Il8R02 -0.24781111 0.063570890
## c4_Il8R06 -0.00321172 -0.059835956
## c4_Il8R17 -0.19534144 0.041277013
## c4_Il8R27 0.03333787 0.074139077
## c4_Il8R39 0.09518824 0.157357581
## c4_Il8R40 -0.25397890 0.065088054
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.10029758 -0.029870866
## 21_HF_PFOS 0.09048186 0.002264925
## 21_LF_CTRL 0.01976239 0.020269575
## 21_LF_PFOS -0.12172060 -0.046839167
## 8_HF_CTRL 0.06535997 0.026255098
## 8_HF_PFOS -0.01683624 -0.003710718
## 8_LF_CTRL 0.05927658 -0.029732112
## 8_LF_PFOS -0.17869504 0.017313010
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.029992 0.0042845 0.6411 0.719
## Residuals 37 0.247269 0.0066830## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.1321 0.02469 1.1118 0.273
## feed 1 0.2536 0.04742 2.1351 0.043 *
## PFOS 1 0.1583 0.02959 1.3323 0.176
## day:feed 1 0.0996 0.01861 0.8382 0.535
## day:PFOS 1 0.0961 0.01796 0.8089 0.630
## feed:PFOS 1 0.1159 0.02168 0.9760 0.384
## day:feed:PFOS 1 0.0983 0.01838 0.8275 0.579
## Residual 37 4.3954 0.82168
## Total 44 5.3493 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Ileum wuf data..."## Warning in betadisper(dist.used, mdat[, VAR]): some squared distances are
## negative and changed to zero
## $sites
## PCoA1 PCoA2
## c1_Il21R10 -0.01552500 -0.041157543
## c1_Il21R20 -0.12356955 -0.025910710
## c1_Il21R22 -0.17648056 0.021794202
## c1_Il21R24 -0.23593996 -0.075359722
## c1_Il21R32 0.01349228 0.101549982
## c1_Il21R44 0.18566320 -0.093601734
## c1_Il21R48 -0.07784087 -0.013346384
## c1_Il8R14 -0.23166607 -0.055850561
## c1_Il8R29 0.19351785 -0.078523738
## c1_Il8R37 0.23745954 -0.061324319
## c2_Il21R09 -0.08096174 -0.027064235
## c2_Il21R21 -0.23143438 -0.071145224
## c2_Il21R31 0.17919016 0.093121642
## c2_Il21R33 0.15526292 0.101449265
## c2_Il21R36 0.09425306 0.030239883
## c2_Il21R43 0.03438167 -0.032419608
## c2_Il21R45 0.04710632 0.047370722
## c2_Il8R03 0.13256883 0.067375133
## c2_Il8R18 -0.20733215 -0.052483043
## c2_Il8R28 0.24071991 -0.123642309
## c2_Il8R30 0.22721576 -0.116030225
## c3_Il21R07 -0.17960318 -0.028743171
## c3_Il21R08 -0.20155722 -0.041552654
## c3_Il21R11 -0.16694337 -0.030814078
## c3_Il21R35 0.19588502 -0.091847931
## c3_Il8R05 -0.09102899 0.066499635
## c3_Il8R13 -0.23896399 -0.026231429
## c3_Il8R16 -0.18561132 -0.032608356
## c3_Il8R25 0.05253459 0.272306525
## c3_Il8R26 0.16576272 0.107968032
## c3_Il8R38 0.06897566 -0.050850115
## c3_Il8R41 0.06145924 0.003756657
## c3_Il8R42 0.23334623 -0.122161988
## c4_Il21R19 -0.21629701 -0.048354474
## c4_Il21R23 -0.21816869 0.019422941
## c4_Il21R34 0.11798416 0.242241372
## c4_Il21R46 0.21491850 -0.114646278
## c4_Il21R47 -0.12308739 0.157849651
## c4_Il8R01 -0.22099472 0.040666602
## c4_Il8R02 -0.13531422 0.025080153
## c4_Il8R06 0.14758984 -0.013206327
## c4_Il8R17 -0.02256495 -0.020917832
## c4_Il8R27 0.18773227 0.063394281
## c4_Il8R39 0.13004607 -0.040110089
## c4_Il8R40 0.06381953 0.067817399
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.12879126 0.077489622
## 21_HF_PFOS 0.05627354 0.006042275
## 21_LF_CTRL -0.14931323 -0.032695114
## 21_LF_PFOS -0.20470905 -0.042725603
## 8_HF_CTRL 0.19822512 -0.038622115
## 8_HF_PFOS 0.12560818 -0.041311749
## 8_LF_CTRL -0.06663548 0.046049300
## 8_LF_PFOS -0.19684665 -0.041689670
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 7 0.047171 0.0067388 0.8838 0.5287
## Residuals 37 0.282126 0.0076250## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * feed * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.06984 0.03446 2.7036 0.069 .
## feed 1 0.76652 0.37817 29.6727 0.001 ***
## PFOS 1 0.11574 0.05710 4.4803 0.018 *
## day:feed 1 0.03473 0.01713 1.3443 0.201
## day:PFOS 1 0.01849 0.00912 0.7157 0.518
## feed:PFOS 1 0.02700 0.01332 1.0451 0.318
## day:feed:PFOS 1 0.03881 0.01915 1.5025 0.195
## Residual 37 0.95580 0.47155
## Total 44 2.02692 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""## [1] "Processing Ileum_HF bray data..."
## [1] "No extra plots..."## Warning in betadisper(dist.used, mdat[, VAR]): some squared distances are
## negative and changed to zero
## $sites
## PCoA1 PCoA2
## c1_Il21R32 0.29586294 -0.149669225
## c1_Il21R44 -0.20492171 0.049701583
## c1_Il21R48 0.26266328 0.034394407
## c1_Il8R29 -0.21075364 0.011838708
## c1_Il8R37 -0.30666980 -0.037240994
## c2_Il21R31 0.05001624 -0.241487324
## c2_Il21R33 0.09913815 -0.085248676
## c2_Il21R36 0.10773893 -0.002751269
## c2_Il21R43 0.31130373 0.446247857
## c2_Il21R45 0.16449560 -0.075870609
## c2_Il8R28 -0.40074944 0.054298623
## c2_Il8R30 -0.34729667 0.046752262
## c3_Il21R35 -0.22173976 0.119582749
## c3_Il8R25 0.19211265 -0.131752284
## c3_Il8R26 0.09418400 -0.281485144
## c3_Il8R38 0.02250071 0.071237556
## c3_Il8R41 0.09322456 -0.035943351
## c3_Il8R42 -0.37925602 0.071517280
## c4_Il21R34 0.13076647 0.277128186
## c4_Il21R46 -0.31180234 0.040020038
## c4_Il21R47 0.48267828 0.159104165
## c4_Il8R27 -0.01450770 -0.218381747
## c4_Il8R39 -0.08362514 0.024466744
## c4_Il8R40 0.17463668 -0.146459535
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.08641527 -0.04756695
## 21_HF_PFOS 0.09800798 -0.01628586
## 8_HF_CTRL -0.19029484 -0.03792191
## 8_HF_PFOS -0.06359309 0.03335053
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.00058 0.000194 0.0052 0.9995
## Residuals 20 0.74947 0.037474## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.17469 0.05600 1.3268 0.214
## PFOS 1 0.22315 0.07154 1.6948 0.127
## day:PFOS 1 0.08819 0.02827 0.6698 0.658
## Residual 20 2.63329 0.84419
## Total 23 3.11932 1.00000
## [1] ""
## [1] "Processing Ileum_HF jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_Il21R32 -0.04354129 -0.33606480
## c1_Il21R44 0.07501218 -0.35755632
## c1_Il21R48 -0.04747928 -0.36122710
## c1_Il8R29 -0.37270792 -0.25492786
## c1_Il8R37 -0.29287587 -0.20797572
## c2_Il21R31 0.25238437 -0.05768245
## c2_Il21R33 0.11088671 0.13974637
## c2_Il21R36 -0.10735466 0.15591865
## c2_Il21R43 0.16273840 0.03287798
## c2_Il21R45 0.14714026 0.14343478
## c2_Il8R28 0.31274214 -0.10434220
## c2_Il8R30 0.21988009 -0.01339328
## c3_Il21R35 0.07291330 0.05370034
## c3_Il8R25 0.05853915 0.14810534
## c3_Il8R26 -0.15120604 0.17741463
## c3_Il8R38 -0.14114760 0.20288552
## c3_Il8R41 0.05165636 0.18008826
## c3_Il8R42 0.04844101 0.08659716
## c4_Il21R34 0.22370638 0.05060556
## c4_Il21R46 -0.36196109 0.07304761
## c4_Il21R47 0.33870522 -0.05870783
## c4_Il8R27 -0.22269920 0.08414993
## c4_Il8R39 -0.01528729 0.06028752
## c4_Il8R40 -0.31848533 0.16301793
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.09383410 0.004623938
## 21_HF_PFOS 0.03351044 0.023607736
## 8_HF_CTRL -0.01416662 0.023067382
## 8_HF_PFOS -0.09608269 -0.006716635
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.009676 0.0032254 0.8151 0.5006
## Residuals 20 0.079144 0.0039572## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.2535 0.04564 1.0323 0.388
## PFOS 1 0.1990 0.03583 0.8104 0.739
## day:PFOS 1 0.1901 0.03424 0.7743 0.823
## Residual 20 4.9108 0.88429
## Total 23 5.5534 1.00000
## [1] ""
## [1] "Processing Ileum_HF unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_Il21R32 0.03582995 -0.20441292
## c1_Il21R44 0.10749176 -0.13648848
## c1_Il21R48 0.03608849 -0.17934873
## c1_Il8R29 -0.43255182 0.05127845
## c1_Il8R37 -0.12314222 -0.17298622
## c2_Il21R31 0.14892466 -0.08577998
## c2_Il21R33 0.10802840 0.16393554
## c2_Il21R36 -0.15851031 0.04822860
## c2_Il21R43 0.08239697 -0.06619507
## c2_Il21R45 0.01737078 0.23013052
## c2_Il8R28 0.23905644 0.05583611
## c2_Il8R30 0.14247397 -0.12530853
## c3_Il21R35 0.05638689 -0.05594774
## c3_Il8R25 0.08336501 -0.03300091
## c3_Il8R26 -0.08594355 0.11676414
## c3_Il8R38 -0.12485087 -0.03534898
## c3_Il8R41 0.12749368 0.05243894
## c3_Il8R42 0.10032254 -0.04934061
## c4_Il21R34 0.19651928 0.15096814
## c4_Il21R46 -0.33351818 -0.02981092
## c4_Il21R47 0.26813170 0.14333186
## c4_Il8R27 -0.14052588 0.10338030
## c4_Il8R39 0.03837183 0.01577172
## c4_Il8R40 -0.38920949 0.04190477
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.0740774558 -0.01024614
## 21_HF_PFOS 0.0607155262 0.01618628
## 8_HF_CTRL 0.0003696179 0.02477129
## 8_HF_PFOS -0.0556104706 -0.06881162
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.011919 0.0039731 0.5409 0.6598
## Residuals 20 0.146910 0.0073455## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.18301 0.06481 1.4782 0.122
## PFOS 1 0.07548 0.02673 0.6097 0.890
## day:PFOS 1 0.08938 0.03165 0.7220 0.782
## Residual 20 2.47615 0.87682
## Total 23 2.82402 1.00000
## [1] ""## [1] "Processing Ileum_HF wuf data..."
## [1] "No extra plots..."## Warning in betadisper(dist.used, mdat[, VAR]): some squared distances are
## negative and changed to zero
## $sites
## PCoA1 PCoA2
## c1_Il21R32 0.138531149 -0.027087189
## c1_Il21R44 -0.125551683 -0.028581473
## c1_Il21R48 0.094936758 -0.116219237
## c1_Il8R29 -0.119015754 0.004308111
## c1_Il8R37 -0.133039017 0.045539945
## c2_Il21R31 0.035169881 0.066084815
## c2_Il21R33 0.056819375 0.046106580
## c2_Il21R36 0.033509998 -0.023349704
## c2_Il21R43 0.020340082 -0.147279640
## c2_Il21R45 0.074492906 -0.029523971
## c2_Il8R28 -0.186977784 0.012665534
## c2_Il8R30 -0.172758570 0.019281999
## c3_Il21R35 -0.131621227 -0.003331130
## c3_Il8R25 0.235798456 0.216336489
## c3_Il8R26 0.053544241 0.080441164
## c3_Il8R38 -0.026750530 -0.073071232
## c3_Il8R41 0.029373062 -0.045414620
## c3_Il8R42 -0.182918320 0.021216941
## c4_Il21R34 0.159515283 0.093682332
## c4_Il21R46 -0.163840108 0.015374061
## c4_Il21R47 0.272572425 -0.147093532
## c4_Il8R27 0.006566974 0.055893529
## c4_Il8R39 -0.051238919 -0.017012500
## c4_Il8R40 0.082541323 -0.018967274
##
## $centroids
## PCoA1 PCoA2
## 21_HF_CTRL 0.05124490 0.02600011
## 21_HF_PFOS 0.03407592 -0.04486237
## 8_HF_CTRL -0.09945812 0.02821815
## 8_HF_PFOS -0.04911372 -0.03351384
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.006879 0.0022931 0.1984 0.8963
## Residuals 20 0.231198 0.0115599## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.04311 0.05268 1.2476 0.232
## PFOS 1 0.06334 0.07739 1.8330 0.107
## day:PFOS 1 0.02090 0.02554 0.6050 0.712
## Residual 20 0.69112 0.84440
## Total 23 0.81848 1.00000
## [1] ""
## [1] "Processing Ileum_LF bray data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_Il21R10 -0.16320320 -0.054824497
## c1_Il21R20 0.03156841 -0.060666742
## c1_Il21R22 0.07012180 0.237778968
## c1_Il21R24 0.22029659 -0.099861867
## c1_Il8R14 0.18279089 -0.063872989
## c2_Il21R09 -0.04150796 -0.062138181
## c2_Il21R21 0.20895766 -0.090637286
## c2_Il8R03 -0.54417031 -0.047530819
## c2_Il8R18 0.15499567 -0.056873863
## c3_Il21R07 0.10031724 0.029084141
## c3_Il21R08 0.16477992 -0.013690438
## c3_Il21R11 0.09322591 -0.036964019
## c3_Il8R05 -0.14726401 0.170200609
## c3_Il8R13 0.11652679 -0.067968382
## c3_Il8R16 0.10726685 0.014388920
## c4_Il21R19 0.16409202 -0.008068341
## c4_Il21R23 0.03091342 0.085530984
## c4_Il8R01 0.01674380 -0.003132598
## c4_Il8R02 -0.01371067 0.180602496
## c4_Il8R06 -0.57900162 -0.088314548
## c4_Il8R17 -0.17373920 0.036958451
##
## $centroids
## PCoA1 PCoA2
## 21_LF_CTRL 0.05255558 -0.02660162
## 21_LF_PFOS 0.13645570 -0.01897033
## 8_LF_CTRL -0.17593316 0.09832854
## 8_LF_PFOS 0.11936957 -0.03305287
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.067775 0.022592 2.228 0.1221
## Residuals 17 0.172377 0.010140## [1] "PERMANOVA RESULTS FOR: bray"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.17869 0.12476 3.4322 0.026 *
## PFOS 1 0.25392 0.17728 4.8771 0.014 *
## day:PFOS 1 0.11462 0.08002 2.2015 0.123
## Residual 17 0.88507 0.61794
## Total 20 1.43229 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Ileum_LF jac data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_Il21R10 -0.34732908 -0.17717946
## c1_Il21R20 -0.34209574 -0.18548438
## c1_Il21R22 -0.27752644 -0.22036457
## c1_Il21R24 -0.38897189 -0.11086483
## c1_Il8R14 -0.14091875 -0.29020155
## c2_Il21R09 -0.04970128 0.20109239
## c2_Il21R21 -0.02352256 0.18962572
## c2_Il8R03 0.27321590 -0.04182373
## c2_Il8R18 -0.18047465 0.27104568
## c3_Il21R07 0.01928149 0.06623487
## c3_Il21R08 0.28910350 -0.12166444
## c3_Il21R11 0.24239650 -0.09227632
## c3_Il8R05 0.21909947 -0.10140330
## c3_Il8R13 -0.07906633 0.22761264
## c3_Il8R16 -0.03937382 0.09598058
## c4_Il21R19 0.30937388 -0.10762956
## c4_Il21R23 0.35141873 -0.15368258
## c4_Il8R01 0.14309172 0.12396194
## c4_Il8R02 -0.07760575 0.23143821
## c4_Il8R06 0.16938296 0.02535005
## c4_Il8R17 -0.06977787 0.17023263
##
## $centroids
## PCoA1 PCoA2
## 21_LF_CTRL 0.06788923 -0.02348932
## 21_LF_PFOS -0.10576707 -0.10872933
## 8_LF_CTRL 0.14660111 0.04695118
## 8_LF_PFOS -0.09816315 0.12743767
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.021961 0.0073203 1.0392 0.4004
## Residuals 17 0.119752 0.0070443## [1] "PERMANOVA RESULTS FOR: jac"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.2382 0.05379 1.1122 0.291
## PFOS 1 0.2937 0.06630 1.3709 0.149
## day:PFOS 1 0.2559 0.05776 1.1944 0.218
## Residual 17 3.6415 0.82215
## Total 20 4.4293 1.00000
## [1] ""
## [1] "Processing Ileum_LF unif data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_Il21R10 -0.14605871 0.1455284080
## c1_Il21R20 -0.16606131 -0.0922987968
## c1_Il21R22 -0.14693601 -0.1232355349
## c1_Il21R24 -0.33959365 0.1326765281
## c1_Il8R14 0.05362501 -0.1087221358
## c2_Il21R09 -0.05765618 -0.0304891015
## c2_Il21R21 -0.13082895 -0.1578012848
## c2_Il8R03 0.28502789 0.0108154016
## c2_Il8R18 -0.26412048 0.0378208714
## c3_Il21R07 -0.00181096 0.1955984626
## c3_Il21R08 0.28577256 0.0595150332
## c3_Il21R11 0.25489112 0.0757322328
## c3_Il8R05 0.22756796 -0.0539025051
## c3_Il8R13 -0.22272276 0.0051840353
## c3_Il8R16 -0.05267236 -0.0002514994
## c4_Il21R19 0.29636272 0.0150219305
## c4_Il21R23 0.34552372 0.0799265785
## c4_Il8R01 0.06963577 -0.0710835329
## c4_Il8R02 -0.17125776 -0.1139811223
## c4_Il8R06 0.09439349 -0.1537267986
## c4_Il8R17 -0.21308112 0.1476728300
##
## $centroids
## PCoA1 PCoA2
## 21_LF_CTRL 0.07677005 0.09273085
## 21_LF_PFOS -0.06740939 -0.05650311
## 8_LF_CTRL 0.11213937 -0.07721753
## 8_LF_PFOS -0.16564168 0.02403808
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.020704 0.0069012 1.0186 0.4089
## Residuals 17 0.115179 0.0067753## [1] "PERMANOVA RESULTS FOR: unif"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.07961 0.03405 0.7133 0.679
## PFOS 1 0.20326 0.08693 1.8211 0.071 .
## day:PFOS 1 0.15799 0.06757 1.4155 0.162
## Residual 17 1.89746 0.81146
## Total 20 2.33833 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
## [1] "Processing Ileum_LF wuf data..."
## [1] "No extra plots..."
## $sites
## PCoA1 PCoA2
## c1_Il21R10 -0.095515415 9.871690e-02
## c1_Il21R20 0.013784885 5.316491e-02
## c1_Il21R22 0.012584734 -1.253042e-02
## c1_Il21R24 0.135039437 2.583151e-02
## c1_Il8R14 0.110281974 -2.865509e-03
## c2_Il21R09 -0.027510833 6.804244e-02
## c2_Il21R21 0.128209288 2.180199e-02
## c2_Il8R03 -0.287302495 -5.700351e-03
## c2_Il8R18 0.097028709 1.044557e-02
## c3_Il21R07 0.056387557 2.046966e-02
## c3_Il21R08 0.084230247 8.263639e-03
## c3_Il21R11 0.053437705 2.492796e-02
## c3_Il8R05 -0.100103555 -4.404493e-02
## c3_Il8R13 0.063816809 -7.376267e-02
## c3_Il8R16 0.058906982 9.149932e-03
## c4_Il21R19 0.100270187 2.862295e-03
## c4_Il21R23 0.009155307 -1.187293e-01
## c4_Il8R01 0.013413297 -1.358245e-01
## c4_Il8R02 -0.023843687 6.085975e-06
## c4_Il8R06 -0.299539533 -3.261710e-02
## c4_Il8R17 -0.102731599 8.239187e-02
##
## $centroids
## PCoA1 PCoA2
## 21_LF_CTRL 0.03988042 0.0312079605
## 21_LF_PFOS 0.08165593 0.0070083848
## 8_LF_CTRL -0.11226480 -0.0412948838
## 8_LF_PFOS 0.07518297 -0.0001709307
##
## attr(,"class")
## [1] "ordiplot"
## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 3 0.017830 0.0059433 1.7475 0.1953
## Residuals 17 0.057816 0.0034009## [1] "PERMANOVA RESULTS FOR: wuf"
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ day * PFOS, data = mdat, permutations = 999, na.action = na.omit)
## Df SumOfSqs R2 F Pr(>F)
## day 1 0.05419 0.12637 3.5239 0.037 *
## PFOS 1 0.07703 0.17964 5.0095 0.013 *
## day:PFOS 1 0.03619 0.08439 2.3533 0.094 .
## Residual 17 0.26142 0.60961
## Total 20 0.42884 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] ""
SPECIAL FIGURES (Combined Alpha- and Beta-diversity)
The following contained code and content for creating Figures for the main article and Appendix A.
Figure 6: Faecal Alpha & Beta Diversity
params <- readRDS("R_objects/Adiv_params.RDS")
load("scripts/adiv.Rdata")
# Load rdata files with scfa plots
div.plots <- c("plots/adiv/timeline/adiv_figures.Rdata","plots/bdiv/timeline/Feces_HF_no0/PCoA_plot_Feces_HF_no0.Rdata")
lapply(div.plots, load,.GlobalEnv)## [[1]]
## [1] "p.obs" "p.eve" "p.sha" "p.fpd" "p.all"
##
## [[2]]
## [1] "bray.perm" "bray.plot" "jac.perm" "jac.plot" "unif.perm" "unif.plot"
## [7] "wuf.perm" "wuf.plot"# rm_legend <- function(p){p + theme(legend.position = "none")}
#Renaming bdiv HF plots
hf.bray.perm <- bray.perm
hf.bray.plot <- rm_legend(bray.plot)
hf.jac.perm <- jac.perm
hf.jac.plot <- rm_legend(jac.plot)
hf.unif.perm <- unif.perm
hf.unif.plot <- rm_legend(unif.plot)
hf.wuf.perm <- wuf.perm
hf.wuf.plot <- rm_legend(wuf.plot)
# Load bdiv LF plots
load("plots/bdiv/timeline/Feces_LF_no0/PCoA_plot_Feces_LF_no0.Rdata")
#Renaming bdiv HF plots
lf.bray.perm <- bray.perm
lf.bray.plot <- rm_legend(bray.plot)
lf.jac.perm <- jac.perm
lf.jac.plot <- rm_legend(jac.plot)
lf.unif.perm <- unif.perm
lf.unif.plot <- rm_legend(unif.plot)
lf.wuf.perm <- wuf.perm
lf.wuf.plot <- rm_legend(wuf.plot)
load("plots/bdiv/timeline/Feces_no20/PCoA_plot_Feces_no20.Rdata")
legend <- get_legend(bray.plot)
#remove leftovers
rm(bray.perm,bray.plot,jac.perm,jac.plot,unif.perm,unif.plot,wuf.perm,wuf.plot)
p.adiv <- ggarrange(p.obs,p.sha,p.fpd,
nrow = 1,
labels = c("A","",""),
common.legend = TRUE,
legend = "top",
font.label = list(size = 24, face = "bold"))
p.adiv
p.bdiv <- ggarrange(hf.bray.plot, hf.jac.plot, lf.bray.plot, lf.jac.plot,
ncol = 2, nrow = 2,
align = "hv",
label.x = 0,
font.label = list(size = 24, face = "bold"),
labels = c("B","C","D","E"))
p.bdiv
# Save combined graphics
ggsave(filename = "plots/figures/Figure 6 - diversity_combined_bray_jac.png", p.all, device = "png", dpi = 300, height = 350, width = 350, units = "mm")
ggsave(filename = "plots/figures/Figure 6 - diversity_combined_bray_jac.pdf", p.all, device = "pdf", dpi = 300, height = 350, width = 350, units = "mm")
# clear the environment and release memory
rm(list = ls(all.names = TRUE)[ls(all.names = TRUE) != "params"])
invisible(gc())Figure A.1: Day 0
# Load and process Day 0 beta-diversity for both diets
params <- readRDS("R_objects/params_betadiv.RDS")
#load("R_objects/bdiv_bray_Feces.RData")
# Choose metric
METRICES <- c("bray","jac","unif","wuf") #not used for illustration: "unif", "wuf"
# Choose variable
VAR <- "feed_treat"
MTRL <- "Feces"
DAY <- "d0"
FEEDS <- c("HF","LF")
# Load data
for (FEED in FEEDS) {
for (METRIC in METRICES) {
print(paste0("Running ",FEED," and ",METRIC))
BFILE <- paste0("R_objects/bdiv_sub_",MTRL,"_",DAY,"_",FEED,"_",METRIC,".Rdata")
if (METRIC == "unif") {
load(BFILE)
dist.used <- unif.sub.dist
nmds.used <- unif.sub.nmds
pcoa.used <- unif.sub.pcoa
phy.used <- phy.sub
rm(unif.sub.dist, unif.sub.nmds, unif.sub.pcoa, phy.sub)
} else if (METRIC == "wuf") {
load(BFILE)
dist.used <- wuf.sub.dist
nmds.used <- wuf.sub.nmds
pcoa.used <- wuf.sub.pcoa
phy.used <- phy.sub
rm(wuf.sub.dist, wuf.sub.nmds, wuf.sub.pcoa,phy.sub)
} else if (METRIC == "bray"){
load(BFILE)
dist.used <- bray.sub.dist
nmds.used <- bray.sub.nmds
pcoa.used <- bray.sub.pcoa
phy.used <- phy.sub
rm(bray.sub.dist, bray.sub.nmds, bray.sub.pcoa, phy.sub)
} else if (METRIC == "jac"){
load(BFILE)
dist.used <- jac.sub.dist
nmds.used <- jac.sub.nmds
pcoa.used <- jac.sub.pcoa
phy.used <- phy.sub
rm(jac.sub.dist, jac.sub.nmds, jac.sub.pcoa, phy.sub)
}
# Extract metadata from phyloseq
mdat <- data.frame(sample_data(phy.used))
# If a variable consist of numbers, but represent distinct groups remember to make it into a factor
mdat[,VAR] <- as.factor(mdat[,VAR])
# Create plots of eigenvalues for PCoA plots
pcoa.tab <- plot_ordination(phy.used, pcoa.used,axes = 1:5,justDF = TRUE)
nmds.tab <- plot_ordination(phy.used, nmds.used,axes = 1:5,justDF = TRUE)
# Reformat tables to create one common table
colnames(nmds.tab)[1:5] <- c("Axis.1","Axis.2","Axis.3","Axis.4","Axis.5")
nmds.tab$ordination <- "nmds"
pcoa.tab$ordination <- "pcoa"
ord.tab <- rbind(nmds.tab,pcoa.tab)
ord.tab[,VAR] <- as.factor(ord.tab[,VAR])
# Melt axis to be in one variable
axis.tab <- pivot_longer(data = ord.tab, cols = c("Axis.1","Axis.2","Axis.3","Axis.4","Axis.5"), names_to = "Axis", values_to = "position")
# Calculate centroids PCOA
centroid.1 <- pcoa.tab %>% group_by(across(all_of("feed_treat_day"))) %>% get_summary_stats("Axis.1", type = "mean")
centroid.1 <- subset(centroid.1, select = -c(variable,n))
colnames(centroid.1)[1:2] <- c("feed_treat_day","X")
centroid.2 <- pcoa.tab %>% group_by(across(all_of("feed_treat_day"))) %>% get_summary_stats("Axis.2", type = "mean")
centroid.2 <- subset(centroid.2, select = -c(feed_treat_day,variable,n))
colnames(centroid.2)[1] <- "Y"
centroid <- cbind(centroid.1,centroid.2)
centroid <- centroid %>% mutate("day" = case_when(grepl("0_",feed_treat_day) ~ "d0",
grepl("8_",feed_treat_day) ~ "d08",
grepl("12_",feed_treat_day) ~ "d12",
grepl("16_",feed_treat_day) ~ "d16",# grepl("20_",feed_treat_day) ~ "d20",
grepl("21_",feed_treat_day) ~ "d21"),
"label" = case_when(grepl("0_",feed_treat_day) ~ "Day 0",
grepl("8_",feed_treat_day) ~ "Day 8",
grepl("12_",feed_treat_day) ~ "Day 12",
grepl("16_",feed_treat_day) ~ "Day 16",
grepl("21_",feed_treat_day) ~ "Day 21",))
centroid <- centroid %>% mutate("feed_treat" = case_when(grepl("HF_CTRL",feed_treat_day) ~ "HF_CTRL",
grepl("HF_PFOS",feed_treat_day) ~ "HF_PFOS",
grepl("LF_CTRL",feed_treat_day) ~ "LF_CTRL",
grepl("LF_PFOS",feed_treat_day) ~ "LF_PFOS"))
centroid <- centroid %>% mutate("coord" = case_when(day == "d0" ~ "x1",
day == "d08" ~ "x2",
day == "d12" ~ "x3",
day == "d16" ~ "x4",
# day == "d20" ~ "x5",
day == "d21" ~ "x5"))
# centroid <- centroid[order(centroid$day),]
# Plot PCoA
pcoa.plot <- ggplot(data = ord.tab[ord.tab$ordination == "pcoa",], aes_string(x = "Axis.1", y = "Axis.2", color = "feed_treat")) +
stat_ellipse(aes_string(x = "Axis.1", y = "Axis.2", color = "feed_treat", fill = "feed_treat"), geom = "polygon", alpha = 0.1, level = 0.9) +
geom_point() +
geom_point(data = centroid, aes_string(x = "X", y = "Y", color = "feed_treat"), shape = 3, size = 4, alpha = 1) +
theme_pubr() +
scale_color_manual(values = params$COL) +
scale_fill_manual(values = params$COL, name = "Feed + Day",
labels = c("HF_d0" = "HF 0","HF_d08" = "HF 8", "HF_d12" = "HF 12", "HF_d16" = "HF 16", "HF_d21" = "HF 21",
"LF_d0" = "LF 0", "LF_d08" = "LF 8", "LF_d12" = "LF 12", "LF_d16" = "LF 16", "LF_d21" = "LF 21"),
breaks = c("HF_d0","LF_d0","HF_d08","LF_d08","HF_d12","LF_d12","HF_d16","LF_d16","HF_d21","LF_d21")) +
facet_wrap(.~feed, labeller = labeller(feed = c("LF" = "LF","HF" = "HF"))) +
scale_y_continuous() +
labs(x = "PCoA 1", y = "PCoA 2") +
guides(color = "none", fill = guide_legend(override.aes = list(alpha = 1, byrow = TRUE, direction = "horizontal")))
print(pcoa.plot)
# Calculate betadispertion
bdisp <- betadisper(dist.used, mdat[,VAR])
print(bdisp)
# Run statical test
ANOVA <- anova(bdisp)
# Run posthoc test if significant and more than two groups
TukeyHSD(bdisp)
plot(TukeyHSD(bdisp))
# Plot dispertion
boxplot(bdisp)
# Perform test
PERM <- adonis2(dist.used ~ treatment, data = mdat, strata = mdat$day, permutations = 999, na.action = na.omit)
print(PERM)
# Save plot
suppressMessages(ggsave(filename = paste0("plots/bdiv/Feces_d0/bdiv_timeline_",FEED,"_",METRIC,".png"), plot = pcoa.plot, device = "png", dpi = 300, units = "mm", height = 200, width = 200))
suppressMessages(ggsave(filename = paste0("plots/bdiv/Feces_d0/bdiv_timeline_",FEED,"_",METRIC,".pdf"), plot = pcoa.plot, device = "pdf", dpi = 300, units = "mm", height = 200, width = 200))
if (FEED == "HF") {
if (METRIC == "bray") {
hf.bray.plot <- pcoa.plot
hf.bray.perm <- PERM
} else if (METRIC == "jac") {
hf.jac.plot <- pcoa.plot
hf.jac.perm <- PERM
} else if (METRIC == "unif") {
hf.unif.plot <- pcoa.plot
hf.unif.perm <- PERM
} else if (METRIC == "wuf") {
hf.wuf.plot <- pcoa.plot
hf.wuf.perm <- PERM
}
} else if (FEED == "LF") {
if (METRIC == "bray") {
lf.bray.plot <- pcoa.plot
lf.bray.perm <- PERM
} else if (METRIC == "jac") {
lf.jac.plot <- pcoa.plot
lf.jac.perm <- PERM
} else if (METRIC == "unif") {
lf.unif.plot <- pcoa.plot
lf.unif.perm <- PERM
} else if (METRIC == "wuf") {
lf.wuf.plot <- pcoa.plot
lf.wuf.perm <- PERM
}
}
}
}## [1] "Running HF and bray"
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = dist.used, group = mdat[, VAR])
##
## No. of Positive Eigenvalues: 18
## No. of Negative Eigenvalues: 5
##
## Average distance to median:
## HF_CTRL HF_PFOS
## 0.2687 0.2772
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 23 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 0.86378 0.43553 0.21966 0.17168 0.09660 0.06568 0.04669 0.04395
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ treatment, data = mdat, permutations = 999, na.action = na.omit, strata = mdat$day)
## Df SumOfSqs R2 F Pr(>F)
## treatment 1 0.02711 0.01328 0.2961 0.959
## Residual 22 2.01428 0.98672
## Total 23 2.04139 1.00000
## [1] "Running HF and jac"
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = dist.used, group = mdat[, VAR])
##
## No. of Positive Eigenvalues: 23
## No. of Negative Eigenvalues: 0
##
## Average distance to median:
## HF_CTRL HF_PFOS
## 0.4002 0.3850
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 23 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 0.9236 0.6786 0.3021 0.2346 0.1948 0.1520 0.1496 0.1331
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ treatment, data = mdat, permutations = 999, na.action = na.omit, strata = mdat$day)
## Df SumOfSqs R2 F Pr(>F)
## treatment 1 0.1324 0.03433 0.7821 0.687
## Residual 22 3.7241 0.96567
## Total 23 3.8565 1.00000
## [1] "Running HF and unif"
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = dist.used, group = mdat[, VAR])
##
## No. of Positive Eigenvalues: 22
## No. of Negative Eigenvalues: 1
##
## Average distance to median:
## HF_CTRL HF_PFOS
## 0.2488 0.2355
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 23 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 0.43375 0.24442 0.11963 0.10237 0.07488 0.07071 0.06298 0.05407
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ treatment, data = mdat, permutations = 999, na.action = na.omit, strata = mdat$day)
## Df SumOfSqs R2 F Pr(>F)
## treatment 1 0.0413 0.02816 0.6375 0.836
## Residual 22 1.4252 0.97184
## Total 23 1.4665 1.00000
## [1] "Running HF and wuf"
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = dist.used, group = mdat[, VAR])
##
## No. of Positive Eigenvalues: 15
## No. of Negative Eigenvalues: 8
##
## Average distance to median:
## HF_CTRL HF_PFOS
## 0.1957 0.2062
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 23 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 0.66770 0.25924 0.11498 0.07046 0.03713 0.03208 0.01882 0.01395
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ treatment, data = mdat, permutations = 999, na.action = na.omit, strata = mdat$day)
## Df SumOfSqs R2 F Pr(>F)
## treatment 1 0.02138 0.01826 0.4092 0.778
## Residual 22 1.14925 0.98174
## Total 23 1.17062 1.00000
## [1] "Running LF and bray"
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = dist.used, group = mdat[, VAR])
##
## No. of Positive Eigenvalues: 19
## No. of Negative Eigenvalues: 4
##
## Average distance to median:
## LF_CTRL LF_PFOS
## 0.3602 0.3469
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 23 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 1.0190 0.7108 0.3194 0.2750 0.2303 0.1863 0.1485 0.1382
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ treatment, data = mdat, permutations = 999, na.action = na.omit, strata = mdat$day)
## Df SumOfSqs R2 F Pr(>F)
## treatment 1 0.1693 0.0511 1.1848 0.288
## Residual 22 3.1429 0.9489
## Total 23 3.3122 1.0000
## [1] "Running LF and jac"
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = dist.used, group = mdat[, VAR])
##
## No. of Positive Eigenvalues: 23
## No. of Negative Eigenvalues: 0
##
## Average distance to median:
## LF_CTRL LF_PFOS
## 0.3803 0.3516
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 23 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 0.9090 0.4185 0.3196 0.2504 0.1708 0.1510 0.1379 0.1270
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ treatment, data = mdat, permutations = 999, na.action = na.omit, strata = mdat$day)
## Df SumOfSqs R2 F Pr(>F)
## treatment 1 0.2352 0.06737 1.5891 0.076 .
## Residual 22 3.2554 0.93263
## Total 23 3.4906 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] "Running LF and unif"
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = dist.used, group = mdat[, VAR])
##
## No. of Positive Eigenvalues: 21
## No. of Negative Eigenvalues: 2
##
## Average distance to median:
## LF_CTRL LF_PFOS
## 0.2139 0.1911
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 23 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 0.26879 0.15886 0.11070 0.07439 0.06731 0.05884 0.05202 0.04698
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ treatment, data = mdat, permutations = 999, na.action = na.omit, strata = mdat$day)
## Df SumOfSqs R2 F Pr(>F)
## treatment 1 0.08905 0.0817 1.9572 0.028 *
## Residual 22 1.00091 0.9183
## Total 23 1.08995 1.0000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] "Running LF and wuf"
##
## Homogeneity of multivariate dispersions
##
## Call: betadisper(d = dist.used, group = mdat[, VAR])
##
## No. of Positive Eigenvalues: 14
## No. of Negative Eigenvalues: 9
##
## Average distance to median:
## LF_CTRL LF_PFOS
## 0.2665 0.2484
##
## Eigenvalues for PCoA axes:
## (Showing 8 of 23 eigenvalues)
## PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 PCoA7 PCoA8
## 1.05912 0.45175 0.11912 0.10319 0.06821 0.05879 0.03898 0.03173
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Blocks: strata
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = dist.used ~ treatment, data = mdat, permutations = 999, na.action = na.omit, strata = mdat$day)
## Df SumOfSqs R2 F Pr(>F)
## treatment 1 0.08231 0.04437 1.0215 0.365
## Residual 22 1.77268 0.95563
## Total 23 1.85499 1.00000
# Save R object
save(hf.bray.plot,hf.bray.perm,hf.jac.plot,hf.jac.perm,hf.unif.plot,hf.unif.perm,hf.wuf.plot,hf.wuf.perm,lf.bray.plot,lf.bray.perm,lf.jac.plot,lf.jac.perm,lf.unif.plot,lf.unif.perm,lf.wuf.plot,lf.wuf.perm, file = paste0("plots/bdiv/Feces_d0/PCoA_plot_feces_day_0.Rdata"))
rm(pcoa.plot,PERM,centroid,centroid.1,centroid.2,bdisp,ANOVA,axis.tab,nmds.tab,nmds.used,phy.used)
# Load alpha-diversity for Day 0
load("scripts/adiv.Rdata")
load("plots/adiv/alpha_d0/adiv_Feces_d0.Rdata")
#Renaming bdiv HF plots
hf.bray.plot <- rm_legend(hf.bray.plot)
hf.jac.plot <- rm_legend(hf.jac.plot)
hf.unif.plot <- rm_legend(hf.unif.plot)
hf.wuf.plot <- rm_legend(hf.wuf.plot)
#Renaming bdiv HF plots
lf.bray.plot <- rm_legend(lf.bray.plot)
lf.jac.plot <- rm_legend(lf.jac.plot)
lf.unif.plot <- rm_legend(lf.unif.plot)
lf.wuf.plot <- rm_legend(lf.wuf.plot)
#remove leftovers
rm(bray.perm,bray.plot,jac.perm,jac.plot,unif.perm,unif.plot,wuf.perm,wuf.plot)## Warning in rm(bray.perm, bray.plot, jac.perm, jac.plot, unif.perm, unif.plot, :
## objekt 'bray.perm' blev ikke fundet## Warning in rm(bray.perm, bray.plot, jac.perm, jac.plot, unif.perm, unif.plot, :
## objekt 'bray.plot' blev ikke fundet## Warning in rm(bray.perm, bray.plot, jac.perm, jac.plot, unif.perm, unif.plot, :
## objekt 'jac.perm' blev ikke fundet## Warning in rm(bray.perm, bray.plot, jac.perm, jac.plot, unif.perm, unif.plot, :
## objekt 'jac.plot' blev ikke fundet## Warning in rm(bray.perm, bray.plot, jac.perm, jac.plot, unif.perm, unif.plot, :
## objekt 'unif.perm' blev ikke fundet## Warning in rm(bray.perm, bray.plot, jac.perm, jac.plot, unif.perm, unif.plot, :
## objekt 'unif.plot' blev ikke fundet## Warning in rm(bray.perm, bray.plot, jac.perm, jac.plot, unif.perm, unif.plot, :
## objekt 'wuf.perm' blev ikke fundet## Warning in rm(bray.perm, bray.plot, jac.perm, jac.plot, unif.perm, unif.plot, :
## objekt 'wuf.plot' blev ikke fundet# Call plots
p.adiv <- ggarrange(p.obs,p.sha,p.fpd,
nrow = 1, ncol = 3,
labels = c("A","",""),
common.legend = TRUE,
align = "hv",
legend = "top",
font.label = list(size = 24, face = "bold"))
p.adiv
p.bdiv <- ggarrange(hf.bray.plot, hf.jac.plot, hf.unif.plot, lf.bray.plot, lf.jac.plot, lf.unif.plot,
ncol = 3, nrow = 2,
align = "hv",
label.x = 0,
font.label = list(size = 24, face = "bold"),
labels = c("B","C","D","E","F","G"))
p.bdiv
p.all2 <- ggarrange(p.obs,p.sha,p.fpd,hf.bray.plot, hf.jac.plot, hf.unif.plot, lf.bray.plot, lf.jac.plot, lf.unif.plot,
ncol = 3, nrow = 3,
align = "hv",
common.legend = TRUE,
legend = "top",
font.label = list(size = 24, face = "bold"),
labels = c("A","","","B","","","C","",""),
heights = c(2,3,3))## Warning: Graphs cannot be horizontally aligned unless the axis parameter is
## set. Placing graphs unaligned.
# Save combined graphics
ggsave(filename = "plots/figures/SUP_Figure A1 - diversity_feces_day_0.png", p.all2, device = "png", dpi = 300, height = 250, width = 300, units = "mm")
ggsave(filename = "plots/figures/SUP_Figure A1 - diversity_feces_day_0.pdf", p.all2, device = "pdf", dpi = 300, height = 250, width = 300, units = "mm")
# clear the environment and release memory
rm(list = ls(all.names = TRUE)[ls(all.names = TRUE) != "params"])
invisible(gc())Figure A.2: ILEUM DIVERSITY
load("scripts/adiv.Rdata")
load("plots/adiv/alpha_d08/adiv_Ileum_d08.Rdata")
# renaming
p.eve.8 <- p.eve
p.obs.8 <- p.obs
p.sha.8 <- p.sha
p.fpd.8 <- p.fpd
load("plots/adiv/alpha_d21/adiv_Ileum_d21.Rdata")
p.eve.21 <- p.eve
p.obs.21 <- p.obs
p.sha.21 <- p.sha
p.fpd.21 <- p.fpd
rm(p.eve,p.sha,p.obs,p.fpd)
load("plots/bdiv/timeline/Ileum_HF/PCoA_plot_Ileum_HF.Rdata")
#Renaming bdiv HF plots
hf.bray.perm <- bray.perm
hf.bray.plot <- rm_legend(bray.plot)
hf.jac.perm <- jac.perm
hf.jac.plot <- rm_legend(jac.plot)
hf.unif.perm <- unif.perm
hf.unif.plot <- rm_legend(unif.plot)
hf.wuf.perm <- wuf.perm
hf.wuf.plot <- rm_legend(wuf.plot)
# Load bdiv LF plots
load("plots/bdiv/timeline/Ileum_LF/PCoA_plot_Ileum_LF.Rdata")
#Renaming bdiv HF plots
lf.bray.perm <- bray.perm
lf.bray.plot <- rm_legend(bray.plot)
lf.jac.perm <- jac.perm
lf.jac.plot <- rm_legend(jac.plot)
lf.unif.perm <- unif.perm
lf.unif.plot <- rm_legend(unif.plot)
lf.wuf.perm <- wuf.perm
lf.wuf.plot <- rm_legend(wuf.plot)
load("plots/bdiv/timeline/Ileum/PCoA_plot_Ileum.Rdata")
legend <- get_legend(bray.plot)
#remove leftovers
rm(bray.perm,bray.plot,jac.perm,jac.plot,unif.perm,unif.plot,wuf.perm,wuf.plot)
# Call plots
p.adiv <- ggarrange(p.obs.8,p.sha.8,p.fpd.8, p.obs.21,p.sha.21,p.fpd.21,
nrow = 2, ncol = 3,
labels = c("A","","","B","",""),
common.legend = TRUE,
align = "hv",
legend = "top",
font.label = list(size = 24, face = "bold"))
p.adiv
p.bdiv <- ggarrange(hf.bray.plot, hf.jac.plot, lf.bray.plot, lf.jac.plot,
ncol = 2, nrow = 2,
align = "hv",
label.x = 0,
font.label = list(size = 24, face = "bold"),
labels = c("C","D","E","F"))
p.bdiv
# Save combined graphics
ggsave(filename = "plots/figures/diversity_ileum_combined_bray_jac.png", p.all, device = "png", dpi = 300, height = 350, width = 350, units = "mm")
ggsave(filename = "plots/figures/diversity_ileum_combined_bray_jac.pdf", p.all, device = "pdf", dpi = 300, height = 350, width = 350, units = "mm")
# clear the environment and release memory
rm(list = ls(all.names = TRUE)[ls(all.names = TRUE) != "params"])
invisible(gc())Figure A.3: CAECUM DIVERSITY
load("scripts/adiv.Rdata")
load("plots/adiv/alpha_d08/adiv_Cecum_d08.Rdata")
# renaming
p.eve.8 <- p.eve
p.obs.8 <- p.obs
p.sha.8 <- p.sha
p.fpd.8 <- p.fpd
load("plots/adiv/alpha_d21/adiv_Cecum_d21.Rdata")
p.eve.21 <- p.eve
p.obs.21 <- p.obs
p.sha.21 <- p.sha
p.fpd.21 <- p.fpd
rm(p.eve,p.sha,p.obs,p.fpd)
load("plots/bdiv/timeline/Cecum_HF/PCoA_plot_Cecum_HF.Rdata")
#Renaming bdiv HF plots
hf.bray.perm <- bray.perm
hf.bray.plot <- rm_legend(bray.plot)
hf.jac.perm <- jac.perm
hf.jac.plot <- rm_legend(jac.plot)
hf.unif.perm <- unif.perm
hf.unif.plot <- rm_legend(unif.plot)
hf.wuf.perm <- wuf.perm
hf.wuf.plot <- rm_legend(wuf.plot)
# Load bdiv LF plots
load("plots/bdiv/timeline/Cecum_LF/PCoA_plot_Cecum_LF.Rdata")
#Renaming bdiv HF plots
lf.bray.perm <- bray.perm
lf.bray.plot <- rm_legend(bray.plot)
lf.jac.perm <- jac.perm
lf.jac.plot <- rm_legend(jac.plot)
lf.unif.perm <- unif.perm
lf.unif.plot <- rm_legend(unif.plot)
lf.wuf.perm <- wuf.perm
lf.wuf.plot <- rm_legend(wuf.plot)
load("plots/bdiv/timeline/Cecum/PCoA_plot_Cecum.Rdata")
legend <- get_legend(bray.plot)
#remove leftovers
rm(bray.perm,bray.plot,jac.perm,jac.plot,unif.perm,unif.plot,wuf.perm,wuf.plot)
# Call plots
p.adiv <- ggarrange(p.obs.8,p.sha.8,p.fpd.8, p.obs.21,p.sha.21,p.fpd.21,
nrow = 2, ncol = 3,
labels = c("A","","","B","",""),
common.legend = TRUE,
align = "hv",
legend = "top",
font.label = list(size = 24, face = "bold"))
p.adiv
p.bdiv <- ggarrange(hf.bray.plot, hf.jac.plot, lf.bray.plot, lf.jac.plot,
ncol = 2, nrow = 2,
align = "hv",
label.x = 0,
font.label = list(size = 24, face = "bold"),
labels = c("C","D","E","F"))
p.bdiv
# Save combined graphics
ggsave(filename = "plots/figures/diversity_cecum_combined_bray_jac.png", p.all, device = "png", dpi = 300, height = 350, width = 350, units = "mm")
ggsave(filename = "plots/figures/diversity_cecum_combined_bray_jac.pdf", p.all, device = "pdf", dpi = 300, height = 350, width = 350, units = "mm")
# clear the environment and release memory
rm(list = ls(all.names = TRUE)[ls(all.names = TRUE) != "params"])
invisible(gc())Figure A.4: Alternative representations
load("plots/bdiv/timeline/Feces_no020/PCoA_plot_Feces_no020.Rdata")
# Call plots
p1 <- ggarrange(bray.treat,jac.treat,bray.diet,jac.diet,
ncol = 2, nrow = 2,
align = "v",
font.label = list(size = 24, face = "bold"),
labels = c("A","B"),
common.legend = TRUE)
p1
# Save combined graphics
ggsave(filename = "plots/figures/Figure_A4_Separation_bray_jac.png", p1, device = "png", dpi = 300, height = 180, width = 350, units = "mm")
ggsave(filename = "plots/figures/Figure_A4_Separation_bray_jac.pdf", p1, device = "pdf", dpi = 300, height = 180, width = 350, units = "mm")
# clear the environment and release memory
rm(list = ls(all.names = TRUE)[ls(all.names = TRUE) != "params"])
invisible(gc())SETTINGS
Overview of the parameters and packages that were used for this Rmarkdown.
PARAMETERS
The following paramenters were set in for this analysis:
params <- readRDS( "R_objects/params_betadiv.RDS")
tmp <- unlist(params)
dat <- data.frame(Parameter = names(tmp), Value = unname(tmp))
kbl(dat, row.names = F) %>% kable_classic(lightable_options = "striped")| Parameter | Value |
|---|---|
| input | R_objects/Phyloseq.Rdata |
| metrics | bray|jac|unif|wuf|ait |
| COL.LF_CTRL | #a5cee3 |
| COL.LF_PFOS | #1778b6 |
| COL.HF_CTRL | #b4d88a |
| COL.HF_PFOS | #30a148 |
| COLFEED.LF | #1778b6 |
| COLFEED.HF | #30a148 |
SESSION INFO
The analysis was run in the following environment:
## R version 4.3.1 (2023-06-16 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=Danish_Denmark.utf8 LC_CTYPE=Danish_Denmark.utf8
## [3] LC_MONETARY=Danish_Denmark.utf8 LC_NUMERIC=C
## [5] LC_TIME=Danish_Denmark.utf8
##
## time zone: Europe/Copenhagen
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggrepel_0.9.4 vegan_2.6-4 lattice_0.22-5
## [4] permute_0.9-7 ggExtra_0.10.1 cowplot_1.1.1
## [7] phyloseq_1.44.0 kableExtra_1.3.4 ggpubr_0.6.0
## [10] GMHmicrobiome_0.1.0 lubridate_1.9.3 forcats_1.0.0
## [13] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
## [16] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
## [19] ggplot2_3.4.4 tidyverse_2.0.0
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-7 gridExtra_2.3 rlang_1.1.1
## [4] magrittr_2.0.3 ade4_1.7-22 compiler_4.3.1
## [7] mgcv_1.9-0 systemfonts_1.0.5 vctrs_0.6.5
## [10] reshape2_1.4.4 rvest_1.0.3 pkgconfig_2.0.3
## [13] crayon_1.5.2 fastmap_1.1.1 ellipsis_0.3.2
## [16] backports_1.4.1 XVector_0.40.0 labeling_0.4.3
## [19] rmdformats_1.0.4 utf8_1.2.3 promises_1.2.1
## [22] rmarkdown_2.25 tzdb_0.4.0 ragg_1.2.6
## [25] xfun_0.41 zlibbioc_1.46.0 cachem_1.0.8
## [28] GenomeInfoDb_1.36.1 jsonlite_1.8.8 biomformat_1.28.0
## [31] highr_0.10 later_1.3.1 rhdf5filters_1.12.1
## [34] Rhdf5lib_1.22.0 broom_1.0.5 parallel_4.3.1
## [37] cluster_2.1.6 R6_2.5.1 bslib_0.6.1
## [40] stringi_1.8.2 car_3.1-2 jquerylib_0.1.4
## [43] Rcpp_1.0.11 bookdown_0.37 iterators_1.0.14
## [46] knitr_1.45 IRanges_2.34.1 httpuv_1.6.12
## [49] Matrix_1.6-4 splines_4.3.1 igraph_1.5.1
## [52] timechange_0.2.0 tidyselect_1.2.0 rstudioapi_0.15.0
## [55] abind_1.4-5 yaml_2.3.7 miniUI_0.1.1.1
## [58] codetools_0.2-19 plyr_1.8.9 shiny_1.8.0
## [61] Biobase_2.60.0 withr_2.5.2 evaluate_0.23
## [64] survival_3.5-7 xml2_1.3.6 Biostrings_2.68.1
## [67] pillar_1.9.0 carData_3.0-5 foreach_1.5.2
## [70] stats4_4.3.1 generics_0.1.3 RCurl_1.98-1.13
## [73] S4Vectors_0.38.1 hms_1.1.3 munsell_0.5.0
## [76] scales_1.3.0 xtable_1.8-4 glue_1.6.2
## [79] tools_4.3.1 data.table_1.14.8 webshot_0.5.5
## [82] ggsignif_0.6.4 rhdf5_2.44.0 grid_4.3.1
## [85] ape_5.7-1 colorspace_2.1-0 nlme_3.1-164
## [88] GenomeInfoDbData_1.2.10 cli_3.6.1 textshaping_0.3.7
## [91] fansi_1.0.5 viridisLite_0.4.2 svglite_2.1.2
## [94] gtable_0.3.4 rstatix_0.7.2 sass_0.4.8
## [97] digest_0.6.33 BiocGenerics_0.46.0 farver_2.1.1
## [100] htmltools_0.5.7 multtest_2.56.0 lifecycle_1.0.4
## [103] httr_1.4.7 mime_0.12 MASS_7.3-60